- The X-Men's first mission is confronting Magneto when he tries to seize control of the missiles stores at the Cape Citadel military base in Florida. Public opinions are mixed.
- The Vanisher attempts to take over Washington D.C. but is defeated by the X-Men. He escapes before he can be arrested.
- The first Sentinels (Mark I) show up during a televised debate between Professor Charles Xavier and Dr. Bolivar Trask. The Sentinels soon try to take over the world under the control of Mastermold. The X-Men stop them along side the repentant Dr. Trask, who dies in their destruction.
- During a conflict with Count Nefaria, the leader of the Maggia crime family, the X-Man recruit known as Thunderbird defied Professor Xavier's orders and tried to prevent the villain's escape. Thunderbird attacked Nefaria's escape plane until it exploded, killing him. This led to Thunderbird's younger brother to seek revenge against Xavier and the X-Men who he believed to be responsible for his brother's death.
- The X-Men come into conflict with Mr. Sinister and his minions the Nasty Boys several times as the geneticist tries to kidnap several mutant children. Several of these children become students at the school.
- Emma Frost and her Hellions battle the X-Men a few times when the X-Men try to stop their more terrorist-leaning actions and their forceful attempts to recruit young mutants into their ranks.
- Dazzler is recruited to the X-Men after she helps the team defeat some anti-mutant thugs at one of her concerts that the X-Men were attending.
- When a handful of students are kidnapped by Genoshan forces, the X-Men fly to the island and team up with Magneto's newly formed Acolytes to overthrow the anti-mutant Government and rescue those that were kidnapped.
- The X-Men travel to Egypt when a young college student is kidnapped by a classmate. The kidnapper turns out to be the villain known as the Living Monolith and the victim is revealed to be Cyclops' long lost brother Alex Summers. The X-Men rescue Alex but he decides to stay in Egypt because he can't control his powers.
- Calvin Rankin learns the secret identities of the X-Men and blackmails his way onto the team as it's leader. Despite a turn towards the more heroic side, Mimic's arrogance leads to him fighting the original five X-Men. After the fight, he loses his memories of the secret identities and disappears.
- Angel is kidnapped again while in the city. He's taken to the tunnels under New York City and held captive by the Morlocks. The X-Men mount a rescue mission but are also captured. Storm challenges the Morlock leader Callisto to battle and wins, becoming the leader of the Morlocks and freeing her team. Storm appoints Callisto the leader of the Morlocks while she is away and the X-Men forge an alliance with the underground mutants.
- An alliance between the X-Men and Avengers is formed.
- The X-Men have a brief conflict with Alpha Flight over Wolverine.
- The school is attacked by allies of Emma Frost's sister to keep the X-Men from coming to the aide of the Hellions while she destroys their school.
- Sentinels (Mark II) were used by Larry Trask, Bolivar Trask's son to attack the X-Men for capture. His programming was flawed however, and young Trask was killed by his own creations when they discovered him a mutant. Cyclops then convinced the Sentinels to fly into the sun, making them believe that destroying the sun would destroy all mutants. At the same time, Stephen Lang was using the Trask research data to create his own Sentinels (Mark III), which went in use publicly and were of a large size, just like the Mark II's. They are sponsored by the government, but certain individuals have their own dark agendas behind the program. Xavier's School for Gifted Youngsters is destroyed as a result. The X-Men currently active at the time are kidnapped and taken to a government space station while students scatter. On the station they encounter several mutants that had been captured by Sentinels as well such as Havok and Polaris. Some join forces with the X-Men upon escape and others return to their lives. While escaping, Jean almost dies and joins with the Phoenix - so it is believed. The new Sentinels once more turn on their creators and are destroyed by the X-Men.
- As the school above is rebuilt, the X-Men and the students they found are based in the bunkers under the school.
- Xavier finishes rebuilding the school and calls it Xavier's Institute. The fact it is a mutant school has become public knowledge since the Sentinels attack, and is open for new recruitments. The X-Men are teachers, and Generation X is created. Not all former X-men and students return though, some opting to take time away from the school and some others just unable (or unwilling) to be found.
- The X-Men encounter The Brood, parasitic alien invaders. With the help of Ms. Marvel, they defeat the hostile aliens.
- The X-Men for a 'quiet' alliance with S.H.I.E.L.D. as a consultant group. Nick Fury provides them some protection against the U.S. Government. It becomes public knowledge that the X-Men are associated with Xavier's Institute. The X-Men start performing guest appearances and become a public icon of mutant and human equality.
- Emma Frost soon joins Xavier's Institute after performing much soul searching. Things are tense at the school and in the X-Men which she has joined.