Well one side lives on a rock outside of San Fransisco and recently had their numbers shredded to maybe a hundred people between all the deaths since House of M and Wolverine of all people deciding that kids shouldn't fight even though Wolverine's thing is bringing kids along with him so they can reenact Lone Wolf and Cub. Their plan is to rely on the cosmic power of the Phoenix Force, something the story frames as unpredictably violent even though that was only the case in Dark Phoenix Saga where it had its mind messed with by the Hellfire Club and has since then been exclusively used for beneficial purposes by Rachel Summers and Jean Grey.
The other side is a prestigious globally beloved independently financed strike fotce that acted out of a mansion that then moved into a Manhattan sky rise tower. They're mostly clueless on what the Phoenix could do so they ask Wolverine for advice and he tells them that the Phoenix is gonna destroy the planet because he's still mooning over another man's wife. They bring the entire Avengers roster and park the Helicarrier outside so Captain America can interact with Cyclops for maybe the fifth time since the decimation of the Mutant population by an Avenger who recently came back to tell everyone nothing that happened was her fault and tells Cyclops that the Phoenix always ruins things and it killed your wife and Cyclops realizes that Cap hasn't read an X-Men comic since 1981 much like the writers of this event so they start fighting.
Then Iron Man brings out a giant gun that shoots the Phoenix, a sentient cosmic force that directly taps into the lifespan of the universe, causing it to blow up. Fortunately because an Avenger is the one that did this it doesn't make the Phoenix blow up the planet but instead causes it to merge into five new hosts who have "I'm going to go batshit and become the final boss" written on their foreheads. The Phoenix Five quickly round up the Avengers in an evil hell dimension that was later established as a perfectly fine place for Mutants to hide away in when the Inhumans gassed the entire planet sterilizing and killing Mutants en mass while literally nobody on the Avengers cared while the intended Mutant messiah Hope Summers goes to Kun Lun where it turns out the Phoenix is actually part of their mythology because Jason Aaron's favourite thing to do in comics is tie the Phoenix to unrelated Marvel characters to the point of recently establishing it used to date Thor's dad. While this is all going on the Phoenix Five also end world hunger and create clean energy and the remaining Avengers plot to break free from these evil fascists they definitely didn't create with their own actions.
So the Avengers and X-Men mount a oounter attack by recruiting the Hulk who is fortunately dumb enough not to remember that the only member of the Illuminati who didn't vote to shoot him into space is currently on the X-Men's side. A bunch of dumb fight scenes happen where members of the Phoenix Five are defeated one by one which makes the other members absorb their powers and drive them even crazier. Professor Xavier shows up and instantly decides to shut down Cyclops' brain which gets him killed in self defense, which horrifies Cyclops enough that an entire army can now beat him into submission.
The story ends with Cyclops in jail getting lectured by Captain America that even if the fate of every one of his people rested on his shoulders he didn't have to kick up such a fuss about it. Cyclops asks if any new Mutants have been born so Captain America begins screaming in his face and storms out the door and tells him he's going to rot in prison forever for killing a single person in self defense after being forcibly possessed by the Phoenix because the Avengers tried to kill it, but then comes to the conclusion that racism might be a thing so he decides to form the Uncanny Avengers, where Captain America gets to boss around a bunch of Mutants including the one who is supposed to lead the team and includes the Avenger who accidentally decimated the Mutant population.
Cyclops, for his part, does learn from Beast that the Phoenix did its job. There are new Mutant births again.
Then three years later the Inhumans happened WHOOPS goodnight everybody