The Agents of Atlas are superhero terrorists, if that makes sense.
It all dates back to the Golden Age and Atlas Comics. Atlas Comics published a comic called The Yellow Claw, which was about a stereotypical evil Chinese supervillain named Yellow Claw who was always being foiled by a young Chinese-American FBI agent named Jimmy Woo.
Yellow Claw founded a terrorist group called the Atlas Foundation. Jimmy Woo and a group of superheroes took over the Atlas Foundation, and they're now trying to use Yellow Claw's old resources to do good.
So the Agents of Atlas are good guys posing as bad guys. As for what the X-Men are doing with them... it just looks like Atlas is trying to steal Cerebra (probably "for the greater good" and I wouldn't be surprised if they really did intend to give it back), and the groups are about to butt heads.