Erg, the epilogue. It's the same thing we get in The Maze Runner: a memorandum from Ava Paige, the Chancellor of WICKED.
In the memorandum in Scorch Trials, Paige talks about how everyone in WICKED should be optimistic about the results of the trials. Sure, not everything went as planned: Thomas got shot by a random dude, for example, and that wasn't really supposed to happen. But overall, things went pretty well. WICKED was able to collect some of the needed patterns, and every death and sacrifice is crucial to the ultimate outcome.
Oh, and WICKED will totally end up restoring the kids' memories eventually. And they'll tell the kids if they have the Flare or not.
Wow, manipulation at its finest.
The thing about the epilogues in both The Maze Runner and The Scorch Trials is that they're utterly frustrating. WICKED is supposedly good, and we can sort of tell that they're the good guys—after all, it seems like their experimentation is truly for the benefit of the human race.
But on the other hand, these experiments are totally unethical and inhumane. Innocent kids are dying, and a lot of the deaths are planned. These kids' lives are being absolutely ruined by these trials, and we hate WICKED for doing this to them.
Yet with each memorandum, we're brought back to the ultimate task at hand: these kids are being put through these trials so that they can somehow save the human race. So, yeah—we guess these trials sort of have to happen. But we're not happy about it.
Gah, Ava Paige. Why must you create this internal conflict within us?