Plot twists in video games? (plz try to be as spoiler free as possible)

I really liked what Spec Ops: The Line did. Playing it without knowing anything about it is the best, and it's currently in the new Humble Bundle right now for $6 or more so you can try it out without having much to lose.

The [REDACTED] form is dead, insect. Are you afraid? What is it you fear? The end of your trivial existence? When the history of my glory is written, your species shall only be a footnote to my magnificence.

OK, it wasn't that big a twist, but it was a cool reveal. System Shock 2 is an incredible game.

Not sure if I can call it the best but, Brütal Legend loves plot twists.

Knights of the Old Republic.

One of my personal favorites is Legend of Heroes: Trails in the Sky. The game is oh so very subtle about everything going on with the plot behind the scenes so when you finally figure out what is going on it is a complete shock because the subtle hints forshadowing it all blend in perfectly with normal conversation in most cases and even the more obvious stuff is only the tip of the iceberg.

And we'll just say that the series makes you paranoid that about anyone with a portrait may actually secretly be the person pulling the strings behind it all. Because yep, the villain ends up being the last person you'd expect to have been secretly manipulating everyone and is actually a complete asshole putting up a front of being nice and helpful.

Mark of the Ninja. "Who are you talking to ?"
The first BioShock has a by-now famous one.
And the Metal Gear Solid series of course has more twists than actual plot.

Borderlands 2 has a few one. One about Sanctuary, then one about the 1st one, then about the Vault Hunters.. the story actually got really nice.
Kotor 1, ofc
Dust, the Elysian Tail

Would you kindly?

The first Bioshock has been mentioned a couple times already and I'll agree with that, also Bioshock Infinite. Played through it for the first time recently and the ending completely caught me off guard and blew my mind.

The 1st Halo game, after beating Library level, I find out the stupid robot I was helping is actually the main villain. Not really a big plot twist, but that level is hard as hell(the hardest in all game personally). To add more wood in my fire of anger, I was playing in the hardest difficulty.

I hate him, all his friends and family. You all burn in hell!

Video Game "plot twist" = The good guy turns out to be the bad guy -> Rinse and repeat

Mmm, I'm not sure if you could call it a "plot" twist, but it was quite the twist for me. The end of Bastion, right before the final choice is one of the few moments in a game that caught me completely off guard.

I haven't been too far in the Soul Reaver games but I love how Raziel's role seems to change over time, as well as his relationship towards the elder god and Kain.

Should also add Batman: Arkham City to the list. That's a good one.
And that's not counting the minor twists along the way that span the franchise so far...

Bioshock Infinite's. What an ending, left me in awe. Never saw it coming.

One the many that come to mind.
Anachronox, the end.

Braid

Star Ocean: 'Till the End of Time, and God, what a stupid plot twist...

Killer7. Nuf said, really. The end was quite a mindfuck.

Soul Nomad is pretty good has a some nice plot twists, a couple play throughs all around good game to sink some hours into

masseffect u die xD

Enslaved pretty much reveals everything at the end. Quite enjoyed it back when I played it on 360.

I just finished that too but I knew that is coming.

This

Well... After The Wolf Among Us I don't think any game will surprise me in next 2 years.