Professor Xavier is the overall leader while Cyclops is usually the field leader for missions.
After the X-Men defeat Apocalypse, Jim is recruited to the X-Men at the same time as Darkseid kidnaps Wolverine, Jean, and Professor Xavier.
The senior X-Men go with the Justice League when the two Earths are brought together to investigate, and the younger members investigate with the Teen Titans. They then end up fighting Wolverine and the Femme Furies until Wolverine regains his memories. The X-Men then assist the Teen Titans and the Justice League in saving a controlled Jean, Xavier, Superboy, and Raven. Afterwords, they relax at the Mansion.
Knowing the Team
The X-Men then assist the Justice League in a peace talk between the two Earths and succeed. Following that, the X-Men witness Darkseid arriving and asking for help against Brainiac and Apocalypse.
Several X-Men then assisted the Justice League in both fights. Wolverine, Jean, and Jim went with Batman's team to New Genesis to find Orion, which they did after a chase with Lightray. Cyclops, Nightcrawler, and Rogue went with Superman's team to Apokolips to fight Apocalypse. When Apocalypse retreated with Darkseid, They then ended up pulled into an asteroid that was revealed to be Brainiac's base.
The X-Men with Batman manage to convince Orion to help and end up seperated even further when Jim goes with Batman, Wonder Woman, and Orion to face Darkseid while Jean and Wolverine are left with Robin and Starfire to look after the children. Superman's team meanwhile battles Apocalypse and Brainiac until Darkseid knocks them out with his Omega Beams and uses Brainiac and Superman to cause a great storm on New Genesis. This causes another separation when Wolverine has Jean go with the Titans and the children while he stays to help High Father and Lightray. Jean and the others then are given shelter by Forger. The X-Men with Superman then attack Darkseid and Apocalypse, and when Jim arrives, he and Rogue manage to push Apocalypse back into the Eye of Ages while the other X-Men deal with Darkseid and Brainiac. Once Darkseid and Brainiac are stopped, the X-Men reunite on New Genesis where everyone is revealed to be alright.
Liger, Rogue, and Nightcrawler then go with several other heroes to investigate an energy disturbance and end up fighting the Hulk, saving him from the Brotherhood, and then fighting the Hulk again.
The X-Men then joined in fighting Amazo, but he scanned their powers and proved to be a match for all of them until Xavier managed to convince Amazo that Luthor was lying to him. The X-Men then witnessed Amazo fly off to the heavens.
Proteges and the Return of Captain AmericaEdit
The of-age X-Men were later asked by SHIELD Director, Nick Fury, to assist the newly assembled Avengers and the League to save Mayor Kelly from the Red Skull. The mission proved successful with Cyclops and Wolverine following the lead of Captain America and Superman. Meanwhile, the younger X-Men assisted the Titans in fighting Slade, Zod, and Magneto, even after they had forced Liger to join. After several encounters with Superboy and Liger, the X-Men are able to free Liger and Superboy and stop Zod. The League, the Avengers, and the X-Men joined the Titans in celebrating Zod, Slade, Magneto, and Red Skull's defeat.
Only a DreamEdit
The X-Men worked with the League and the Titans to stop a prison break at Stryker's before turning in for the night.
They also worked with the Titans and the League to hold of Dr. Destiny's mental assault until Batman stopped him.