The two boys were separated by the authorities: Alex was adopted, but Scott remained comatose in a hospital for a year. Christopher and Katharine were believed dead. (Actually, they were taken prisoner by the Shi'ar; Katharine soon died but Christopher later became Corsair, leader of the Starjammers, a band of interstellar adventurers.)

On recovering, Scott was placed in an orphanage in Omaha, Nebraska that was secretly controlled by his future enemy Mister Sinister. Years later, as a teenager, Scott began to suffer from severe headaches and eyestrain. He was sent to an eye specialist in Washington, D. C., who discovered that lenses made of ruby quartz corrected the problem. While Scott was visiting a large city, his developing mutant power to project optic force beams finally erupted, bursting forth in an uncontrollable blast that demolished a crane, causing it to drop a huge object towards a terrified crowd. Scott saved the crowd by obliterating the object with another blast, but they turned into an angry mob, thinking he had tried to kill them. Scott fled, ultimately escaping on a freight train.

Professor Charles Xavier and F.B.I. agent Fred Duncan joined forces in their mutual attempt to find Scott. Meanwhile, a mutant known as Jack O' Diamonds, and later as the Living Diamond, forced the frightened boy to aid him in his crimes. Xavier rescued Scott from the Living Diamond and enlisted him as the first member of the team of young mutants he would teach in using their powers, the X-Men.

As Cyclops Scott soon became deputy leader of the X-Men. He fell in love with his teammate Jean Grey, although his reserve and his worries about the dangers of his optic beams prevented him for years from expressing his feelings to her. When the other original X-Men left the team, Cyclops stayed on as deputy leader of the "new" X-Men.

Shortly afterwards the cosmic entity called the Phoenix Force secretly placed Jean in suspended animation and impersonated her, adopting a form identical to hers. When this Phoenix committed suicide, Scott believed that the real Jean had died and he left the X-Men. Eventually he returned to the team and met and married Madelyne Pryor, a woman who was Jean's double; he was unaware she was a clone of Jean created by Mister Sinister. Scott and Madelyne had a baby son, named Nathan Christopher, and Scott again left the X-Men.

Subsequently, the real Jean Grey emerged from suspended animation. Scott left his wife and joined with Jean and the other original X-Men in founding a new team, the original X-Factor. Madelyne went insane, developed superhuman powers, and perished in combat with Jean Grey.

Later, Apocalypse infected Nathan with a techno-organic virus. To save his life, Scott was forced to allow a time traveling member of the Askani cult to transport Nathan to the 30th century of an alternate future.

After Professor Xavier returned from a long sojourn in space with the Starjammers, Cyclops and the other X-Factor members rejoined the X-Men. Ever since then Cyclops has remained with the X-Men, sharing deputy leadership with Storm.

Scott and Jean were finally married. While they were on their honeymoon, Mother Askani, leader of the Askani cult, drew their spirits two millennia into an alternate future, where they inhabited new bodies. There, as Slym and Redd, they spent years raising young Nathan into his early adolescence. Then Scott and Jean returned to their own time and bodies, and Nathan remained to grow up into his time's greatest hero, Cable.