After beating the game I have a few questions maybe some other fans can answer for me.
 

Well im not exactly sure but let me lend my speculation.  
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1) This has to be a plain plot hole that leads into why pigsy must die and gives him a reason to tag along
2) there apparantly is not any autopilot as they made us believe pigsy drove the machine all the way to pyramid. So when the count down was happening, i guess they wanted to make it so he has to steer into the enemy. Granted he only dies because they wanted him too, he could have easily escaped. But then wouldnt he be a third wheel? 
3)thats something i dont understand, were they trying to gather everybody to become part of the virtual world? if so, in the beginning when monkey asked the guard about where his gear was, why did HE die or more importantly why was he conscious to the real world?

I hope someone who understands the ending can shed some light on this.
 
If these plot hole, which are the basis for the entire game, are there, should the game's story be so highly praised?

1. Sounds about right.

2. I think he needed to move the leviathan far enough away (since it can only be driven manually) so they were out of the blast radius.

3. They are capturing people, and killing anyone who tries to stop them from doing so. The slaver machines were trying to kill you to prevent what you ended up doing at the end of the game, breaking Pyramid. 

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3. They are capturing people, and killing anyone who tries to stop them from doing so. The slaver machines were trying to kill you to prevent what you ended up doing at the end of the game, breaking Pyramid. 

"

No worries. 

It took me a couple of minutes while the credits rolled to put everything into perspective. Neat way to round up the story, I had no idea where it was going until those last few scenes.

"Boom!  This is what I was missing.  I got mixed up at the end because the message was that Pyramid wasn't killing people, it was saving them.  Thanks for the help.   Anyone else get a little confused"? 

"I also would've liked a little more closure with what Monkey and Trip did after they left Pyramid."

The story is up for grabs, but

" @nick_verissimo said:

"I also would've liked a little more closure with what Monkey and Trip did after they left Pyramid."

Aside from the "turn it back on" moment (which put goosebumps on my arm, sooooo good), I can agree that some more closure there would've been nice.  I mean, what now?  What are they going to do?  Was it the right thing to do?  I just finished the story today.  It was good.  Were there plot holes and arbitrary, contrived pieces to serve the plot?  Sure.  Did I care?  No.  The performances were genuinely great and the characters were highly memorable.  Also, Trip was goddamn addictive HOT!!! "

I figure Pigsy will be back.. just as a complete robot, he'd be so pleased.