The Turians send out a distress call. When we go to help, we find no Turians. It’s a Collector ship, seemingly abandoned. Turns out this is the ship that shot up the Normandy two years ago. The Collectors have a particular interest in Shepard.
We wander through the deserted vessel. A pile of dead human bodies, pods for carrying immobilized people, and evidence of science experiments are gruesome and creepy. At a certain point, though, we see a dead Collector on the lab table. Our Normandy computer is able to access the data. This Collector shares an exact and specific DNA match with the Protheans.
It’s quite the gobsmack. Apparently the Protheans didn’t go extinct. They were subsumed by the Reapers and modified over time.
Of course when we get to the command center after our trip through the ship we learn it’s all been a trap. The Collectors faked the Turian distress signal. Here comes Harbinger to battle us the entire way back to our shuttle.
And, of course, the Illusive Man knew all along that this was a trap. He’s tired of waiting for random Collector attacks. He’s using us as bait to move the quest along. It’s despicable and untrustworthy, but what are we going to say? Please let another colony be ravaged first? He’s got us over a barrel and he knows it. The mission was a resounding success, and we’d look mighty petulant if we carried on with a grudge.