|Five, Episode 1-16|
|Air date||Never Aired|
- "Thanks to you all, we have averted catastrophe. It was not without its price, however. But steel is forged through fire, and like it we have been made stronger. We are prepared for what the future brings. I know this, because I have glimpsed into the mind of Apocalypse. Many challenges still await us. But I saw some who have been our enemies become friends. And with a heavy heart, I saw the dearest of friends, become the most terrible of enemies. I saw my X-Men grow and change. And of course, I saw that some people never change. But one thing was clear...that no matter what awaits us, terrible or wonderous... the X-Men will always be there, ready. And of that, I am proud."
- —Charles Xavier
The series ends with a speech by Charles Xavier, who had caught a glimpse of the future while being controlled by Apocalypse. Boyd Kirkland confirmed that the unproduced fifth season would have expanded on several of these plot threads, with Dark Phoenix being the season's main villain. The following future scenarios were foreseen:
- Continued anti-mutant sentiments.
- A reformed Magneto becomes the teacher of the New Mutants, including a returned Jubilee and Wolfsbane.
- Jean Grey becomes possessed by the almighty and all-powerful Phoenix Force and transforms into the Dark Phoenix. Had the series continued, the show's next season would have focused on the "Phoenix/Dark Phoenix Saga". (Note: It's unknown whether the Phoenix would have been a cosmic entity or a part of Jean's mind as similar to the films and originally in the comics).
- The future X-Men team consisting of adult versions of Cyclops, Nightcrawler, X-23, Iceman, Beast, Shadowcat, Colossus, Rogue (able to fly and not wearing gloves) and Storm. However, Jean Grey and Wolverine are notably absent (Jean was shown in a separate scene, apparently turning into Phoenix) the uniforms these future X-Men wear look very much like the dark uniforms seen in the Ultimate X-Men comic, as well as that of the live-action feature films.
- Adult versions of the Brotherhood, including Pyro, join S.H.I.E.L.D.'s Freedom Force.
- An attack fleet of Sentinels led by a Super Sentinel, which is hinted to be Nimrod. Though Bastion and Mastermold have been suggested.
- The last scene shows the X-Men, the New Mutants, Gambit and Colossus (both former Acolytes) Boom Boom, Havok, Angel, X-23 and Spyke.
- The next season was in talks of bringing in Emma Frost and Psylocke, and Jean Grey as The Phoenix
- If the show had not been canceled, the foreshadowing of Jean Grey becoming the Dark Phoenix, a possible arrival of Scott's father, Corsair, Magneto officially allying himself with Xavier, David Haller and Apocalypse returning, the arrival of the Shi'ar, Madelyne Pryor, Mister Sinister, Bishop, Cable and Rachel Summers (from the present and future; although in the current timeline, Nathan and Rachel are twins whereas the others are not.), and Scott Summers' romance and marriage with Jean Grey.