I did something like this for Eclipse Phase.

The players woke up in shitty pod sleeves, with no memory of the last 4 years, and people after them trying to kill them. They found out that they worked doing sensitive operations for corps, and they were always loaded up with a backup after the mission and given their pay, and the fork with all the memories of the mission is deleted (to protect the company's secrets).

They found out there were 6 jobs that had "issues" recently, and they needed to found out who the jobs were for, what the jobs were, and what went wrong in them.

After a while, they discovered that the memories of their mission were not deleted, and were instead put into secure backup sites. The players then had to break into these secure sites, and retrieve their memories of each mission.

When they got a set of memories, instead of just telling them what happened, I had them play out the mission. There was a bit of meta-gaming trying to find clues, but it honestly didn't matter.

I could have went several different ways with the big reveal at the end, but I chose to have it be that one of the first of the "bad" missions was actually because they decided as a group that they wouldn't let the corp get away with what they did, and they never came back in to be deleted. All the times they were fighting mysterious enemies in all the missions and in trying to find information, they were actually fighting themselves.

They had to figure out if their other selves were right, or if they had gone crazy, and there was a lot of issues about who had the rights to actually be who they were.

In the end they decided to stick it to the guy responsible, but they didn't really do much to expose the corp (the corp had a lot of plausible deniability on their side, and could also level a lot of blame on the PCs, who had been duped for a good while into being accomplices).

TL;DR: Eclipse Phase, because that's its bread and butter.