Main Plot
This story takes place right after Season 2 of Young Justice (Invasion). The team is operating side by side with the Justice League and gained society's recognition. The government has accepted them and granted them permission to operate as government's defense just as regular police officers or judges. Salvage and Darkseid has teamed up and the team is investigating the Light's plans (along with research on Wally's death) not aware of Darkseid's assistance. Lex Luther has replaced Tseng as UN Secretary-General in the last episode in Invasion where he has gained the role of dictatorship and the public's trust.
On the X-Men side, this story is influenced from the X-Men evolution universe. There isn't a direct placement for this storyline based off of Evolution, but between the sentinel project before the Apocalypse sections is where the influence comes in. The most important aspect is that the character designs and traits are heavily influenced from Evolution. Society isn't as fond of mutants as they are of the Young Justice team. In fact, society hates them. The X-Men's main mission is to gain the public's trust while still saving the innocent. It's time for the public to start accepting them, both the team and Charles know that. In this universe, Quick Silver did not save Magneto from the sentinel like in the show so he has died. Mystic now leads a small group of the brotherhood. Besides trying to gain the public's trust, the brotherhood is still a problem for the X-Men, and soon, both the X-Men and Young Justice teams and their universes will collide.
I want to give my friend Devin credit for giving me the idea for the story.