One of the most important moments in Cyclops' life happened in the X-Men comics in 2000 when the hero merged with the villainous Apocalypse.  This storyline would go on to play a major role in upcoming arcs, taking Scott Summers out of the X-Men line-up for a short while.

During the Apocalypse: The Twelve arc, which spanned across multiple X-Men comic books, Apocalypse sought to assemble 12 of the universe's most powerful mutants. These 12 mutants were: Magneto, Polaris, Storm, Sunfire, Iceman, Bishop, Mikhail Rasputin, Professor X, Cyclops, Jean Grey, Cable and the Living Monolith.

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the twelve

By kidnapping The Twelve and siphoning off their power, Apocalypse could ascend to godhood, putting the entire universe at stake. By his own logic, Polaris and Magneto represented opposing magnetic poles; Cyclops, Jean and Cable represented the family unit; Bishop and Mikhail represented time and space; Storm, Iceman and Sunfire were the elements of nature; Xavier was the mind and the Living Monolith was the core.

After kidnapping The Twelve, he placed them in his machine, planning to use the Living Monolith to siphon the other 11 mutants' power, subsequently granting him omnipotence. Apocalypse had a hidden 13th factor: Nate Grey. As the most powerful mutant alive, Apocalypse needed Nate's body to be a host for his own.

After The Twelve escape Apocalypse's machine, they realize they are almost too late. Apocalypse has already started to transfer himself into Nate's consciousness. To save his friends, the universe and his son, Cyclops jumps in front of Apocalypse's beam. This act disrupts his transfer into Nate's body, but instead, Scott and Apocalypse merged, much to the horror of the X-Men.

This event kickstarted "Ages of Apocalypse," in which, Apocalypse (now merged with Cyclops), uses his powers to disrupt time and space. He warps reality, resulting in a few issues of X-Men comics that explored alternate realities. These realities included one where Gambit and Storm were members of the Original 5 X-Men, dystopian futures, and one where Wolverine, Hulk, Ghost Rider and Spider-Man fill in for the Fantastic Four after the original team is presumed dead.

By the end of the "Ages of Apocalypse" arc, Charles says he can no longer sense Scott's consciousness at all, declaring him dead. However, a few months later, the miniseries X-Men: The Search for Cyclops would prove him wrong.

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In this miniseries, Scott is experiencing a bad case of amnesia, living in Morocco and unaware of who he is. It's revealed that he has been holding back Apocalypse but occasionally slips out of control and frees the monster. These moments of darkness leave Scott petrified, questioning the nature of his moral compass.

As Jean and Cable embark on a rescue mission to save Scott, Apocalypse's loyalists are also trying to track him down. Scott and Apocalypse battle for control throughout the series until finally, Jean Grey is able to separate his consciousness from Apocalypse. Cable makes quick waste of Apocalypse, but the ending is far from happy.

Scott wrestled with his inner demons for months, feeling isolated and frightened by the darkness that lurked inside him after his time merged with Apocalypse. Grant Morrison's New X-Men series touched on Scott's psyche after this event a little more, noting how the hero was haunted by the experience.

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