In the final part explaining what happened between 6 months ago and M-Day, Jay's wings were cut off but he doesn't let Elixir heal him. After they find him, Emma calls all of the students into the Danger Room for an insane free-for-all brawl to see who's worthy of jumping up to X-Man levels. However, this is all just a ruse so that she can try to kill off X-23. Scott walks in on the brawl and stops it, also circumventing Emma's attempt to cut Laura off the team.
In the present day, after all of the human students are asked to leave the school, they say their final goodbyes... before being blown up by a rocket presumably originating from William Stryker's followers.