Proteus has finally confronted his father, but Joe McTaggert decides to runaway. So does Wolverine as his form being manipulated has caused him to fear Proteus. This gets him even more confused, and it's just another failed attempt for the X-Men to capture Proteus. However, when Proteus tries confronting his father a second time, Xavier allows himself to be absorbed so Proteus can also see his memories. Through this, the boy was able to tame his powers and have his father accept him with open arms.
So the ending was happy. It was a classic text book, happily ever after ending though. It was just too perfect, and they didn't even reveal the results of the voting! So Xavier said Proteus will be able to control his powers, making it sound like it'll take an entire process, though he instantly learns to not turn into his lava like form and hug his father. And it seems too convenient that Joe McTaggert decides to accept his son after being absent in his life for a decade and a half. At least Wolverine was funny again. He wasn't as comical as the previous installment, but his cowardly actions were just as amusing.