" @FLStyle: >>Juno and Minerva are two different beings. Minerva was in ACII and Juno in ACB. Your "Juno (Minerva?)" makes it look like you think otherwise, which is not the case << Earlier in this thread there was discussion of who the diety was.  It was not exactly clear in the storyline who was talking to Desmond.  >>The Cross meaning Templars has been common knowledge since ACII << Never said it wasn't.  People are not connecting the dots though.  Everyone seems to think this is some cryptic cliff hanger ending.  It really is not.   Anyway, none of this changes the fact that the 72 days clue coupled with the last day you play as Desmond being 10 Oct 2012 is an obvious storyline tie in to Mayan Calendar doomsday predictions in the real world... and that was the point of my post. "

• It is clear who was talking to Desmond, it was Juno. Here's Juno and here's Minerva.
• It didn't seem that way to me.
  
• I understand what the point of your post was, the point of my post was that I didn't want people taking some of your mistakes as fact.
  

I'm not so convinced Lucy is a Templar, or "the cross" Juno eludes to. It could be any Templar (or representation thereof, say, such as the supposed Animus in which Desmond might be at that moment). Though admittedly it seems likely to be someone within Desmond's camp. 
The implications are there for those who want to read that into it, certainly, but I think it's a red herring. Everything Lucy has stood for up to this point goes against her betraying Desmond. It could be her plan. But I think if that was Ubi's intention all along, they'd have foreshadowed it craftier than "Lucy is a Templar, posing as an Assassin, posing as a Templar"' making us retroactively rethink all she's done to help the Assassins, and I don't think that line of reasoning holds much water as of yet. 
 
But, again, I will admit it remains a safe assumption that Juno could very well mean Lucy is the cross. But can we be sure that when Juno states "She lies not within our sight. The cross darkens the horizon" she isn't alluding to The Ones' inability to see "her" and not Desmond's? I mean, if they know who the girl is then why not mention more about her, or give Desmond clear direction? 
Maybe Desmond is in a Templar run Animus as himself, and "she is not within our sight" because Lucy isn't really there at all, only Desmond in an Animus. Maybe they had Desmond kill virtual Lucy, intentionally glitching/hacking his DNA's memory in order to put him into shock, getting him out of the Templars' animus, even for a moment. He clearly says "No" after the two male voices decide to jack him back in. That could mean anything, but he's clearly not happy about going back in, wherever he is and whoever those dudes are.
Just spit-ballin' here. Not sold on any of this really. But what say you? 
 

And for those still unclear, that is most definitely Juno and not Minerva, or Minerva under one of her many names. FLStyle's link above illustrates that pretty clearly. But I think people are getting that twisted (as I did at first) because they are both played by the same voice actor (and are of course both female holograms of Those Who Came Before). 

Last quick points:  

1. We know Adam and Eve are not the only humans at that point, as they stole the POE in an attempt to free the human slaves we see in the Truth video of ACII, therefor many today would not have descended from them.
2. I believe Subject 16 is truly dead, and he is simply the literal representation of the proverbial "Ghost in the Machine". Nothing more. How much consciousness this entails I'm not so sure, but he certainly knows who Desmond is and whose side he's on.
3. In ACII Minerva mentioned she and some of her kind were the ones who knew to turn away from war, suggesting there are those who didn't. I suppose this means the Templars have their own "gods" guiding them (?).

I took the speech from Juno to Desmond as meaning that Lucy's death had to occur so that a re-birth could happen.
Juno said that one would accompany Desmond through the gate but he had to go alone because they could not currently see the one they were looking for , 
i.e.  she does not yet exist in Desmond's life but will be "asleep" and waiting for Desmond to awaken her - the missing sixth sense - which could only be possible
after a re-birth of Lucy and a meeting in some future time-space  with Desmond.
Just as Desmond was awakened via the Animus - he will then awaken the next incarnation of Lucy.
I had also seen some chat that the next AC is hinted at taking place in Egypt
Lastly , a few folks on the board need to separate communism from socialism - I think the assassin's ideal in this game is socialistic in nature - a economic system - not communism, a political system with socialistic ideas....but that's just me.

" I'm not so convinced Lucy is a Templar, or "the cross" Juno eludes to. It could be any Templar (or representation thereof, say, such as the supposed Animus in which Desmond might be at that moment). Though admittedly it seems likely to be someone within Desmond's camp. 
The implications are there for those who want to read that into it, certainly, but I think it's a red herring. Everything Lucy has stood for up to this point goes against her betraying Desmond. It could be her plan. But I think if that was Ubi's intention all along, they'd have foreshadowed it craftier than "Lucy is a Templar, posing as an Assassin, posing as a Templar"' making us retroactively rethink all she's done to help the Assassins, and I don't think that line of reasoning holds much water as of yet. 
 
But, again, I will admit it remains a safe assumption that Juno could very well mean Lucy is the cross. But can we be sure that when Juno states "She lies not within our sight. The cross darkens the horizon" she isn't alluding to The Ones' inability to see "her" and not Desmond's? I mean, if they know who the girl is then why not mention more about her, or give Desmond clear direction? 
Maybe Desmond is in a Templar run Animus as himself, and "she is not within our sight" because Lucy isn't really there at all, only Desmond in an Animus. Maybe they had Desmond kill virtual Lucy, intentionally glitching/hacking his DNA's memory in order to put him into shock, getting him out of the Templars' animus, even for a moment. He clearly says "No" after the two male voices decide to jack him back in. That could mean anything, but he's clearly not happy about going back in, wherever he is and whoever those dudes are.
Just spit-ballin' here. Not sold on any of this really. But what say you? 
 

And for those still unclear, that is most definitely Juno and not Minerva, or Minerva under one of her many names. FLStyle's link above illustrates that pretty clearly. But I think people are getting that twisted (as I did at first) because they are both played by the same voice actor (and are of course both female holograms of Those Who Came Before). 

Last quick points:  

1. We know Adam and Eve are not the only humans at that point, as they stole the POE in an attempt to free the human slaves we see in the Truth video of ACII, therefor many today would not have descended from them.
2. I believe Subject 16 is truly dead, and he is simply the literal representation of the proverbial "Ghost in the Machine". Nothing more. How much consciousness this entails I'm not so sure, but he certainly knows who Desmond is and whose side he's on.
3. In ACII Minerva mentioned she and some of her kind were the ones who knew to turn away from war, suggesting there are those who didn't. I suppose this means the Templars have their own "gods" guiding them (?).

"

OK so i signed up to just continue this, but im going to have to agree that desmond is going to look for eve and eventually even go into the animus to actually revisit "the truth" video from assassins creed 2. If you go back and watch the video you can see adam and eve running and looking back constantly, almost like they were looking back at the camera or that the camera was actually a third person they couldnt see because of the way it climbed just like them, but once they actually reach the top of the building that they climb eve says something of the effect of "adam i have it (referring to the apple)" and then you hear some one say "eve" and then both adam and eve turn around in shock and to me that voice sounds like its desmond actually talking to her. what do you guys think?

" I mean, if they know who the girl is then why not mention more about her, or give Desmond clear direction? "

" @bkg4211 said:

" I understand what the point of your post was, the point of my post was that I didn't want people taking some of your mistakes as fact."

" @Damian said:

" I mean, if they know who the girl is then why not mention more about her, or give Desmond clear direction? "

 Oh, come on that is too easy.  If UBI gave up who and where the girl was there would be no reason for us to go out and buy a bunch of copies of AC3.  They are trying to build suspense to support the next game release.  Plus in fantasy adventure literature, the gods always speak in riddles.  It makes the gods seem smarter because you don't understand WTF they mean!     "

Who was the guy Lucy was getting emails from.  William H or something like that?

" Just finished it and I must say... this rocks. Seriously, I love how everything just comes together in some way, then opens up a bunch of more interesting questions.And I have my own little theory to throw in:    

 With what Subject 16 said at the end paired with the voices during the credits lead me to believe that what Desmond (and we) are experiencing are his memories replayed in an Animus. For some reason he is replaying all his memories. When he reaches the memory of stabbing Lucy he goes into shock. This takes him partly out of the Animus program, leading him to hear his "handlers" conversation about how he is in shock, how they have to put him into the Animus to fix it even though it was the Animus that caused it.  To me that makes more sense than him suddenly being somewhere else going into shock.

" @FLStyle said:

" @bkg4211 said:

" I understand what the point of your post was, the point of my post was that I didn't want people taking some of your mistakes as fact."

 Seriously dude, it's a game there are no "facts". None of us know for sure if anything we are saying is accurate or on target.  We're just entertaining ourselves.  That is the beauty of it all, it's a game/fantasy world.  If for some wierd reason people wanted to say "Ezio walks around in a dress looking thingy and swings his hips an awful lot so he must be a tranny" big deal.  If the story works for them that way and makes sense ot them so be it.    It's just like the people who are saying that the Desmond angle is a memory being relived in an animus by yet another person.  It works for them.  I personally interpretted the ending sequence as Desmond had collapsed after stabbing Lucy and they were putting Desmond in the animus to stabilize him.  After reading the "person watching a person watching a person" angle, I liked that and now interpret the story line that way.  It's a story we can take from it what we want.  Even if I am totally off base on the Dec 2012/Mayan calendar thing; you gotta admit it is a cool spin to BS about until AC3 comes out.     "

inception maybe, desmond is placed in a machine to find out where he found eden, but in order to do so, you have make him believe he's helping the good guys, so he has to use an anmus inside an animus to get the clues to the apple.. in the end you couldnt get out of the animus..
 
rambling of a mad man. it it plays out like that.. it would be messed up

 Seriously dude, it's a game there are no "facts".

The Truth will set you free...  

Bitch looked like a fish. not exactly sad to see her go. Interesting that he has to "do it alone"- implies they're not bringing the brotherhood mechanic to ACIII assuming Desmond is the main playable character in that one...and he kinda has to be.

Also, my theory behind it is that I didnt pick up on the "lucy is a templar" thing at all; if so Juno wouldn't then have said "you have to do it alone"- the rest of the assassins could help. As it is he left the other two behind as well, implying that the rest of the order cannot help desmond. 
I saw it more as a "there must be a balance" thing, where he has to kill Lucy in order to save the world- he can't have both, so one must be sacrificed. Doesn't entirely make sense but idk where the Lucy is a templar thing is coming from. 
Also, the Truth message implies that either Lucy's death gives Desmond some power/ability, either literal or mentally, or is a double meaning and the actual pieces of eden matter far less than what Desmond/the Templars will do with it...which is kind of self evident...idk- maybe there is a dual purpose to the pieces, so like the templars can use it to take over and desmond can use it to do something else? idk...so confused. The ending better freaking make sense/ubi better know where they're going, because after ACII the lead guy said even they didn't know how it ended.... assuming they kind of know by now otherwise they wouldn't have done something more drastic.

Alright, I think Desmond isn't in an Animus. I don't think the whole inception animus within an animus makes much sense. As far for the credits, it was after they both collapsed, and the other assassins came and got Lucy and Desmond out of there because obviously the Templars are close on their trail.  
 
I feel like everyone discredits as the other assassins as being there... like at all. I'm sure they saw what happened to Lucy and Desmond after Juno released Desmond/POE. 
 
I think Desmond needed her out of the way. So where shes dead or not, she isn't going to be a hassle for him or an obstacle. He'll have to go on by him self while Shaun and I keep forgetting the chick assassin technician, care for Lucy. 
 
As for William H., he may have died in the first time, when they first tried to save you. I feel kinda bad, considering it must've been just a small group of Assassins against the entire Abstergo security force. 
 
I think the next game will keep the animus, and in fact he'll go back in and probably learn some new skill through the bleeding effect. If it is in Egypt as one person mentioned, possibly the 6th sense that existed with "The ones from before". Because we all know those crazy egyptian had martian drawings on their pyramids. And possibly another temple beneath one of the many pyramids. 
 
I think people are really twisting it WAY past its boundaries. I like the ideas though, its really amazing how far this storyline will push people to figure it out.

" Most interesting thing I got from the Subject 16 stuff (best stuff in the game yet again) was that Capitalism was created by the Templars and Marxism/Communism was created by the Assassins. "

" @damswedon said:

" Most interesting thing I got from the Subject 16 stuff (best stuff in the game yet again) was that Capitalism was created by the Templars and Marxism/Communism was created by the Assassins. "

I definitely got the whole Capitalism being created by the Templars, but I never really got Communism being created by the Assassins. I think it's an interesting route to take either way, I feel like too many games shy away from being political because they fear that they'll lose mass-appeal. "

 
Alot of people say tht desmond had a kid with lucy so she ws preg thn the baby wanted to destroy the world so desmond had to kill the baby   
 
but what i dont understand is that when did desmond and lucy have sex?? 
 
Lets hope we find out in ac3
 
 

OMG!!! Stalin and communism made me think of Fidel Castro and well... since we're talking games, BLACK OPs. and when they assassinate Fidel Castro. The truth is... THEY'RE Assassins!  lol, I'd love to see AC3 make a reference to COD Black Ops or something. THey did it with Mario, I say they need to make fun of some of their competition for the hell of it. 
 
Too bad we can't Snipe Stalin. Personally, I'd love to see Desmond in AC3 get into the animus for a memory from like the Vietnam War or something, and have an ancestor sniper or something lol. With the bleeding effect and an ancestry of assassins and plenty of assassinations in history. Imagine just the 1960's?! Imagine, it'd be weird as hell, but we have Lee Harvey Oswald, Jack Ruby, JFK, ... but since apparently it was a missed shot. So killing JFK was a mistake when really he was going to kill his Templar passenger, The Texas Governor LOL. 
 
Of course he missed >_< . He did go to Russia for a while. Maybe joined the Assassins Guild there? That'd be a sick twist on the whole JFK Assassination. Make Harvey Oswald a good guy! Holy CRAP! Though... he did kill a cop... but hell, we kill random guards in AC1/2/2.5 all the time~!

My theory is  
The next assasins creed you set out to find the Shroud which is a POE which can bring people back to life (or so the fiction suggests) The game will end with bringing lucy back to life somehow and finding out she is pregnant for sure
The next game would be as below ;
If lucy was pregnant or somehow had a baby without any one knowing (no idea what sorta time scale in the real world it is ) Maybe thats what the voices are , Whoever desmond and lucys child is, is in the animus trying to figure out what they have to do to stop the the 2012 stuff because they are a descendant of adam and eve ?

Ok apologies for the length of this, but I have a quite a few questions. I have some speculations on how to interpret the game but I would like some other input. Also apologies if these particular questions have been asked already. I have not yet gone threw the subject 16 puzzles yet…not sure where they are marked on the map  

( anyone who like to enlighten me that would be grand) ….unless they are the whole Romulus thing….anywho I would have just read everyone’s responses but afraid I would read something subject 16 related and spoil it for my self, so if you please indulge me, I would be most grateful.

Ok so Minerva mentions something about Desmonds son being the savior of the world…I was so busy jumping around that I don’t think I truly absorbed it all….but if I did hear her correctly then here are some more thoughts/questions.

I don’t know if any of you recall at the start of the game when Rebecca is having trouble getting   the memory to start  because there is a competing memories…. Lucy says that they ran into a similar situation at Abstergo with a woman who was pregnant….

Could this be Desmon’s sons memories conflicting with his own consciousness? If so how could his son in the future alter Desmonds past, or as we play the game, Desmonds current events?

Anyone have a direct transcript or videos of Minerva’s speeches especially about the whole son bit?

Is it possible that Lucy is pregnant or will be the mother of Desmonds son and because of that Minerva wants her dead? (assuming that the per-humans want to end the world, and that Desmonds son is suppose to be the savior)

Minerva mentions something about Desmond being an abomination part pre-human and part pre-human enemy….Would the enemy be human? Or a certain kind of human ,Assassin vrs templar?

I was unable to hack into the others emails, is this possible?   if so how? And what did the emails contain? Transcripts?

Anyone have the transcript from all Desmonds emails?

Did anyone notice the red glowing path that led from the entrance of the villa where the assassins were hiding out to the assassin symbol ( at the foot of the hill )and down the gated well? Any answers to what that was about?

The little I did venture to read, there seems to be a general consensus that Minerva was saying Lucy could not be trusted…

Evidence supporting that Lucy is up to know good?

Did anyone note that in AC one and two that both main assassin characters were stabbed in the stomach and now in brotherhood our new main assassin, Desmond, stabs Lucy in the stomach? (role reversal)

Also when Cesara was dying and saying that no mortal man could kill him, what was the deal with his body merging with the other body?….who do u think that was?…and do you think that when he had the apple he merged his spirit with it so that he could live on in a predecessor to him self? 

I really hope someone can help me out. If you don’t have the answer now but figure out later feel free to PM me. Thanks again J

PS Sorry for my bad spelling….

After reading some of these posts i have come up with a theory i would like feedback on. 
 
When subject 16 says that Eve's DNA is the key and also mentions Desmond's son, maybe it is not the fact that Desmond is just a replayed memory by his son, but that he and Eve meeting and having a son is the key. Desmond would need her DNA in order to do that (obviously) and subject 16 may be saying it's too late now because she may either be dead or captured.  
 
I'm not really firm on this and it just popped into my head as i was reading some posts. 
 
Also, subject 16 deeply encoded himself into the memories of Ezio and when he mentioned he is running low on energy it may be referring to how much energy he is using up to keep himself hidden from Templar agents.

I'm with what Jeff said in the Bombcast. I really don't know what to feel on the ending. It was still shocking, but not on the same level as Assassin's Creed II. The only thing I know is that the story can go in any direction at this point.

Assassin's Creed is the only franchise of games that with the end of each instalment, as left me saying 'What the f**k'. Brotherhood was no different. The overall story arch is absolutely riveting, having been a deep fan since the first game I'm fascinated with each new piece of information.  
 
Having just completed it, the most interesting part of the ending to me was the voices in the credits. One of which sounded very much like Desmond but slightly different. After I heard that the whole 'your actually a future descendant of Desmond' made more sense. A concept which thrills me to no end, guess Jeff's mad idea might not be so mad after all. Some people are saying that one of the voices could be William, who we know little about. All we know is he as something to do with the Assassin's (we think!). 
 
Concerning the end of the game, it seems the most generally accepted theme at this point is that Lucy is Eve. That's why she was stabbed. Not sure I totally agree with that though. I agree concerning the Subject 16 stuff, that's simply amazing. So glad they go so deep into that conspiracy content stuff. Most games would leave it out and totally ignore it but it seems almost everyone finds it fascinating. One things for certain, we haven't seen or heard the last of Subject 16, that if he is alive or dead is yet to be determined.  
 
God, Assassin's Creed is amazing! 
 
Edit: For those thinking Assassin's Creed 3 could be set in World War Two or in Japanese history, keep in mind that the developers have already stated publicly that they weren't keen at all on WW2 and that setting an AC game in Japan isn't a keen interest either. There's a few articles on the subject about on the web. 

One other thing that's made me feel dumb, but when Subject 16 is talking to Desmond he mentioned a 'son'. Now when I first heard that I thought about the actual Sun, as in the very hot star that powers life on earth. It only occurred to me that he could be talking about Desmond's child after I finished the game, which would add even more backbone to the 'your playing as a future descendant' theory. When you add that, the whole Adam and Eve concept and the voices at the end (in the credits) then it starts to offer one explanation.  
 
Could the one voice be Desmond's child in the future? 
 
BRAIN EXPLODES!

Dudes, it doesn't end with the mayan calendar apocalypse theory. This foreshadowed event is often simply interpreted as the end of the world, while in fact it was said to be the end of an era and the start of a new one. A cataclysm if you will. 
 
In the 1800s, the Theosophic Society was formed by Helena Blavatsky and she wrote The Secret Doctrine, a supposed outline of the history of the universe and mankind. Aside from getting into the literally thousands upon thousands of occult interpretations of symbolism and myth found throughout the history of human consciousness, this is the overarching occult belief system that goes deeper than templars and the illuminati.  
 
Now here's the interesting part - it states existence is a never ending loop of metaphysical unfolding of potential in 7 stages throughout space time, all form and possibility in reality always one. It places us at the peak of the fifth stage, on the fifth earth, as the fifth root race - basically the current highest potential of consciousness in a physical form. Now this shit goes on and on (seriously, this stuff blows even Aleister Crowly out of the water). But what's interesting to me is how at least some aspects of AC point towards this interpretation. This could be intentional or maybe they are alluding to some other bits and pieces of these archetypes echoed elsewhere. 
 
Humans are supposedly the fifth root race - this would make the ancients the fourth. And what lies ahead, unfathomable; the sixth step. There is so much stuff directly pointing to theosophy it's not even funny. The stuff with 72 and the Tetragrammaton? Holy shit. And I expect some people to bog this down to masonic interpretations of the bible and such, but I assure you this shit runs way, way deeper into the recesses of human culture and consciousness.
 
Anyone interested in this should at least check out some videos on Time Wave Zero by Terence McKenna. 
 
But be warned, this is a never ending rabbit's hole of quantum physics, numerology, Jungian psychology and all manner of occult archetypal interpretations of reality. I could list some great books and movies for anyone interested. 
 
And please don't write me off as a new age zealot - first of all new age bullshit is selling the mystique of the occult to mid-life crisis victims in pre-packaged pseudo-science and self-help books. Second - I don't subscribe to any dogma, this stuff is just amazingly fascinating to me. And in the end it doesn't even allow for dogma, as that would be rooted in duality (the cosmos deceiving itself into believing it is separate entities). And it's fun to come at these concept from any angle - philosophical, metaphysical, occult, mathematical, quantum physical, religious, mythological, historical, numerological and archetypes/concepts resonating through poetry, music, architecture or any kind of expression. And it seems Ubisoft agrees with me there, this stuff makes for a great story that goes beyond the Dan Brown stuff that keeps everything fairly grounded. I think at least some folk at Ubisoft have some insight into these old occult works, whether someone is seriously into it and has miraculously convinced hq that it could work as a mainstream action game, or they don't know what to think of it but saw the potential for unique fiction. Either way, it's amazing to me that a game this huge and out there is doing what literature and other media have been struggling to do: getting this stuff any kind of attention at all! Most modern books on this stuff are completely counterculture and directors and musicians hinting to these concepts are often cult as fuck or simply misread as generic symbolism for the sake of symbolism. 
 
/rant

One thing you can definitely guarantee, is that if Minerva/Jupiter(is it?), wanted Lucy to be dead, she is most *certainly* dead. And seeing as they forced him to stab her, I doubt it'd turn out later "naw, we were just playing. We stabbed in you the abdomen just for kicks". 
 
Think about it. The "gods" are not even alive anymore. All of what you see are just projections of their selves - they're completely dead. Yet they knew *exactly* what you were going to do, how you were going to do it, how to guide you there, etc., and they were able to carry on a whole conversation. So really, they planned everything out to the Tee, millenia ago. 
 
As for Communism being from the Assassin's, yeah, I wasn't a big fan of that either. But, they really wanted to do *good*. Look at capitalism and how Abstergo completely controls it and has their arm in every socket known to man. Just like in the Truth videos, where this one guy gets "whacked" by templars, over a tech-support call because his TV was showing his credit card history, predictions, heart rate, schedule, his likes and dislikes absolutely everything you'd need to know about someone. And yet..it's this illusion of freedom. It's like the Matrix really, where you are coerced into thinking that this is real, and because it feels so real, you don't see any problem with The System. And because of that, why would you want to fight it? Or even *think* about fighting it? It's only until you're awakened that you realize there is an issue, and suddenly you want to destroy it all. 
 
I do wonder about Lucy though...I'm beginning to think she might have been a uhm...what is that..a triple agent? Subject 17 said "she can't be trusted". I doubt he was talking about Juno/Minerva, because then he could've just said "dude. don't touch that freaking apple" and he could have been less cryptic ;) 
 
Besides, there isn't anything you could do against the goddesses, since they already know all the moves you will make, the thoughts, etc., long before you've made them. It's like Pre-Crime from "Minority Report". 
 
I am thinking that Subject 17 is actually talking about either a future female character, or Lucy herself. Well, or Rebecca, naturally. 
 
I do wish they'd put more story content into each game. I feel like this is a half-life game...although, I must admit, this is probably what makes it so darn interesting.

" @DJSire said:

" @Ares42 said:

" Well, hmmm.... not quite sure of what to make of the credits... 2 new male voices... "

I got the impression that Desmond is another memory being played out be a descendant... which would make Ezio a memory within a memory, which would be badass. "

  

"

• I think she started off as an assassin but her undercover work at Abstergo may have caused her to start second guessing whether they really were any worse than the Assassins. The emails William sent to her seem to imply she genuinely cares for Desmond's well being which is causing her to be hesitant regarding William's intentions for Desmond back at HQ. During one conversation she mentions having devoted ten years of her life to the Assassin's cause and wanting nothing more now than to help put an end to the conflict. My guess is she gave into temptation and made contact with Abstergo in an effort to try and save Desmond and/or her entire team.

OK so, i signed up for this forum just so i could post in this thread. First off this game was insanely good. This is one of the first game series in a long long time to get better and better with each sequel. I really didn't read every post in this thread so forgive me if any of this was brought up already.  
 
The red trail outside of the sanctuary was a bread crumb trail, in case you got lost you could follow that right back in, everyone with the theory that they were Lucy's footsteps, how would eagle vision know that Lucy's footprints were those of a Templar, but it wouldn't know she was a Templar when looking directly at her in eagle vision.
 
Desmond, I believe was picked up by Templar,  and put back into the animus. There was a definite sense of hostility and haste in the tone of the voice at the end, Abstergo didn't care about the people in the animus, just the information coming out of it, while the assassins seemed concerned throughout the series with the amount of time Desmond spent in the animus. Desmond also had free will and could leave the animus at any time and was not able to at Abstergo, this could be the reason why you cant exit the animus after the end game. 
 
I still don't know what I think about Lucy being a Templar or not, so i have two half assed attempts at theories. The first, she is a Templar, but there is a lot of conflicting pieces in the game if this turns out to be true. Secondly, maybe we shouldn't take what Juno says about the cross darkens the horizon so literally. This is a little off the wall so I'm sure this probably isn't the case but here goes. Everyone knows the story about Jesus and the crucifixion, well maybe Lucy has to die in order to open a gate or a path, both a path and a gate were mentioned in  Juno's bit. In Catholicism the cross represents sacrifice, maybe she had to be sacrificed  in order for Desmond to proceed, whether or not she is resurrected also, remains to be seen. This theory also speaks to the cross "darkening the horizon," the fact that Lucy died makes things look bleak, so to surmise, she is not a Templar, rather an assassin who had to die for some reason which remains to be seen.

Just finished it. poor Lucy :(
 
What's all this talk about Desmond speaking to Subject 16? I never saw that!

" Just finished it. poor Lucy :(  What's all this talk about Desmond speaking to Subject 16? I never saw that! "

" @GunslingerPanda said:

" Just finished it. poor Lucy :(  What's all this talk about Desmond speaking to Subject 16? I never saw that! "

Finish the Subject 16 puzzle ;) "

" @GunslingerPanda: Database > Locations > Filter to Subject 16 > Go find glyphs on all ten buildings in that list. "

I just finished the game a couple of days ago.  Loved it, and like everyone else I'm very excited to see where they take the story next.  After reading this thread to try and answer some of my own questions, I ran across this story... 
 
http://www.huffingtonpost.com/2010/12/13/mona-lisa-gives-more-than_n_796102.html  
 
With all of the talk of the number 72 in the game and elsewhere, just found it interesting to see it come out possibly in Da Vinci's painting.

" @Hamz said:

" @GunslingerPanda: Database > Locations > Filter to Subject 16 > Go find glyphs on all ten buildings in that list. "

Well finishing it before the the game ends gets you a cut scene with demsond and lucy. bad thing is that you can't approach lucy or anyone else because desmond is clipped in the chair, causing me to retstart, don't know if they fixed that "

• Minerva is in Assassin's Creed 2 and Assassin's Creed 2 a lone. Juno is in Brotherhood, Jupiter hasn't been seen yet, he'll probably be in the next one.
• Desmond is Subject 17, you're talking about 16.
  

Desmond is human/god DNA