I still don't really understand how is The Marker related to Necromorph infection. When I played the first game, I though it was an alien device created to keep the infection contained, so when it was lifted from the planet by humans, infection (beggining with the Hive Mind) was released. 
 
But in DS2 it is clear The Marker is actually causing the infection. Can someone sum it up for me? I tried to google it and I found out that the "Red Marker" from original DS was actually a human-made copy and was studdied on Aegis VII, where scientists found out the marks on it's surface are a DNA code for the necromorphs. So, this means the infection actually comes from the marker... so why does it want Isaac to "make them whole again"? What did the Marker get by making Isaac retun it back to the planet? On a recent Bombcast Brad says something about a sphere of influence of the Marker that makes dead bodies go reanimated... so wouldn't be Marker's goal, in first DS, to travel somewhere else and spread the infection, instead of returning to the planet?

 
I think that the simple answer is "We have no clue." 
  
In Dead Space, Dead Nicole tries to get Isaac to return the Marker to the planet and put it on the platform, which apparently causes "dead space" where the Necromorphs can't animate. It was only after Isaac failed to get the Marker into place that the Hive Mind reared its ugly head.  Further, Isaac was apparently assisted along the way by Dead Nicole. In Dead Space 2, Dead Nicole tries to get Isaac into a position where the Marker can be completed; however, it should be noted that it also puts Isaac into a position where the Marker can be destroyed, and what Dead Nicole said was that the Necromorphs needed Isaac's body. Despite hundreds of Necromorphs being in the inner chamber, there was very little effort made by the Necromorphs to reach Isaac once he reached the Marker. 
 
We've got some actions that seem logically incompatible. In both games, the Markers themselves lead Isaac to ending the Necromorph outbreak; in the second game, the Marker goes so far as to commit suicide of sorts in an elaborate fashion. There are a few explanations I can think of though. 
 
In Dead Space: 
A) The Red Marker was a defective copy. While it created Necromorphs and generated insanity in people, it didn't want to do that. It wanted to be stopped, and it manipulated first Dr. Kyne and then Isaac to stop it.  
B) The Red Marker is insane.  Its actions don't make logical sense because it is itself insane. 
C) Isaac's brain was protecting itself by intentionally misunderstanding the Red Marker's message. If the Marker was saying "Don't do A, do B" then Isaac's brain flipped that into "Do A, don't do B." It's still a matter of Isaac going crazy, but it's Isaac going crazy on his own terms rather than those of the Marker.   
D) For the race that created the Markers, "keep Marker on platform" is about the same as "keep control rods in nuclear reactor." Just basic common sense when dealing with something that dangerous. Yes, mishandling the a nuclear reactor leads to the irradiation of the surrounding countryside, yes, mishandling a Marker leads to a Necromorph outbreak, but really, that's what you get for not following proper safety procedures. The Markers were built to interact with creatures with a different brain set-up, and so the warning messages they broadcast out ("WARNING: This device is not properly seated. This may result in Armageddon. Please consult the user manual!")  are not understood properly by the people on the receiving end. Isaac, for whatever reason, is closer to being able to understand the message than most. but it still comes out as garbled. The help pop-up window in the form of Dead Nicole does a poor job of explaining to the human how to fix the problem, and doesn't even have a feedback form.  
 
In Dead Space 2, the best explanation I can think of is similar to that of option C or D on my list above for Dead Space. Dead Nicole was a self-defense mechanism for Isaac's brain, allowing him to externalize the insanity being caused by the Marker. Further, since the part of his brain allocated to Dead Nicole knew how the Marker worked, it pushed him in the direction he needed to go to get there and destroy it.  It's the best explanation I can think of to reconcile the strange behavior of the Markers in both games. To further elaborate, it's possible that the Black Marker itself was flawed, and was dumped in between solar systems, before eventually getting caught up by the passing Sol system and crashing on Earth. Our bad luck to find a broken version, and then copy the flaws. 

It is said the voices that are telling people to kill each other are the nercos. Wile the voices telling you to run is the Markers.  
 
Go read "Dead Space Maryter " or 
 
 WIKI!

I'm more interested in where the Markers actually came from. I can't wait until they unveil some old ancient race of species in the Dead Space uiniverse.

" I'm more interested in where the Markers actually came from. I can't wait until they unveil some old ancient race of species in the Dead Space uiniverse. "

" @Hopefire: Whoa, thats a really interesting perspective. Mucho thanks good sir. XD "

y'know, i would rather not know most of this stuff, i don't really care to know what the game has to tell me, I feel like a horror game stops being scary at all when you understand all of it

Horror comes from not knowing and the more questions they feel compelled to answer the less scary the world will be.

I agree that the developers are intentionally leaving it ambiguous as it adds to the horror and suspense. I am really interested if the species (whether they still exist or the markers are their legacy) behind the markers are apathetic toward other species or malicious. Is the Marker just not compatible with humanity and/or being misused and tampered by humans (per Hopfire's post). Or is the Marker an attempt at immortality by some lost civilization to convert any species that comes into contact with it. Or something even weirder.  
 
I'm really excited to see where this mythos goes. 

They might  have a good explanation of the markers or why the marker acts different between games if they explain that I would be happy. I wouldn't really care if the origin of the Markers was never explained but they should be able to explain the in game stuff in a way that makes sense. I kinda had my own theory of the markers which is that Markers may act as information stores for each planet and when activated send out the signal for the necros, get enough bio mass and then start convergence thus storing the info of the living creatures in the marker. The Marker built by humans and put on Aegis 7 may have thought that was its planet and attempted to get back there and do what it was built for. The one on the Sprawl never moves and so tries to start convergence. Thats what I came up with but I doubt that the writers had a clear idea of the story when they where writing the first game and probably only really established the back story stuff now that  they got a sequel and that it is a big hit.

" Horror comes from not knowing and the more questions they feel compelled to answer the less scary the world will be. "

The Marker emits frequencies that turn people into evil space zombies. I don't really understand it either (what is the purpose of convergence ?) but that's what makes it cool. The first game was scarier because you had no idea what was going on.

Thanks everyone for clarifying there isn't actually a clear explanation of it all. I feel less dumb now.

From what I remember of an audiolog in Dead Space 2, the marker is covered in some kind of blueprints, which it seems to communicate somehow. People of a certain kind of intelligence understand them on some level, but people who can't are driven to madness. That means that aside from turning people into space zombies, the marker is also snow crash. 
 
It's motives, however, are completely alien to me.

Basically we cannot ascertain how they're making Markers, how they're messing the process up, or even really what Markers do in the first place. 
 
So, based on all that, we just have to wait and see. For now its as simple as Necros + Markers = Dead Space.

Judging from what I've been reading on the Dead Space wiki, the Markers we've seen so far are manufactured copies of an Earth artefact called the Black Marker. Altman was the person who revealed it to the public, and for this he was brutally murdered by a Brute and martyred into Unitology. The red markers appear to be made from code that is implanted into people's minds by being in its presence; this is what the "eye poke machine" is for , extracting that data. Red markers appear to suppress the Necromorphs, as on Aegis VII that's what the Marker was planted there for, and why the events of Dead Space occur. Judging by the end of this sequel, though, the Necromorphs are also drawn to it; perhaps to destroy it? They never get near it, though, and the Hive Mind of the Necromorphs appears to be able to "lash out" at afflicted minds through it (the final boss). 
 
Beyond all that, my theories thus far: 
 
By trying to remove the Marker from Aegis VII, they awoke the Necromorph plague, so they may be defensive nodes that trigger the plague when they are disturbed (like how a spider web acts as prey detection for trapdoor spiders and the like) to allow them to gather suitable mass to make a Hive Mind in defense/to spread. It seems the Sprawl was a production facility for Markers (you come across one being assembled near the end, after all), but you never really find out what triggered them to attack; they're clearly aiming for Isaac and Stross (hence the visions both suffer from, where their dead loved ones coax them into giving up or joining them), so it's possible that it sensed biomasses with important information stored in them (ie Isaac and Stross' minds) and attempted to assimilate them. Could it be they need the codes stored in people's minds to create a Hive Mind, and the "Ubermorph" at the end is the remains of Stross after he is absorbed? After all, it has the same sort of head as the one at the end of the first game, and it only appears after Stross dies.