Near the end of Infinite Space for the DS, a big twist is that you and your sister are androids. The setting is sort of like Mass Effect. There's a big space war going on. But you also find out that even more importantly, there are these Overlords (that only a couple people in the universe know about, including the Space Pope) who are god-like aliens responsible for the warp gates (essentially mass relays) that connect the different solar systems. Much like Mass Effect's Reapers, the Overlords plan to destroy all living things to reset the universe once the galactic civilization grows too large.
The main character, Yuri, is apparently an 'Observer', some kind of artificial being whose experiences are relayed back to the Overlords (at least one other major character is confirmed as an Observer); his sister is a 'Tracker', another type of artificial being whose purpose is to be paired with an Observer for some reason that I don't remember. Yuri and his sister's childhood memories were fabricated, and it's implied (though not solidly confirmed) that he and his sister were willed into existence shortly before the beginning of the game, and part of their roles as Observer and Tracker is that they're implanted with a strong bond so they want to care for and protect each other; aside from that intrinsic bond, it is implied that Observers and Trackers otherwise have free will. There are several characters who remember growing up with Yuri and his sister, and it is implied that the Overlords have enough godlike power over reality that they fabricated those memories as well.
As you find this out and Yuri tries to hack into the Overlords' system to find out how to stop them, a defense mechanism kicks in, and the sister (the Tracker), just ceases to exist. There's a flash of light, and instead of her standing there, there's only a lifeless plastic-like faceless android (presumably what was under her skin and flesh all along, though they don't solidly confirm that). Not only that, it's as if she never existed, because suddenly everyone's memory is altered as if Yuri never had a sister. This is near the end of the game, so it's pretty crazy that suddenly everybody acts like they've never heard of this character you've gotten to know for the past like 60-70 hours. It was a pretty powerful moment, because Yuri first has to come to terms with being a pawn of these Overlords and learning his memories are largely false, then losing his sister, then realizing that no one can console him because no one else remembers her.
So yeah, it's almost nothing like Blade Runner, but it's a hell of a curveball in what is already a pretty involved story, with a bunch of interesting space politics and a large cast of characters. Here is more about the story: http://infinitespace.wikia.com/wiki/Story
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