Just as in Book One, the epilogue is structured as a memorandum filed by Ava Paige, the Chancellor of WICKED.
This Memorandum's subject is: "SCORCH TRIALS, Groups A and B" (E.1).
In the report, Ava says that a ton of progress has been made, though not everything went ideally. She expresses a hopeful confidence in the subjects and believes that once everyone's memories have been restored, the subjects will be ready for their tasks.
Ava says that the future of the human race is what really matters and that every death and sacrifice is worth the ultimate outcome.
The Psychs are also deliberating, and when the time's right, they will remove the Swipe and tell the remaining subjects if they're immune or not immune to the Flare.
So, yeah, it seems like WICKED's plan is still going okay, but we'll just have to find out in the next book, won't we?