New story is out: A New Journey.
Explanations of things that happened in A Gamer's Journey:
Ryo: Was growing increasingly untrusting of X-COM, which was further expanded by the Psionic soldiers being used so regularly. And he grew to loath X-COM, and everyone in it. To the point where he discovered a way to contact the aliens, and gave them entrance to X-COM HQ. He believed X-COM to have become too corrupted, and thought the aliens would actually be better rulers than X-COM.
Masambe: After using the device, Masambe saw how the final mission was supposed to end (They would get into the final room. Maxim would kill the Muton's. The others would move in, and over the fight, William would die, and they'd all be badly injured. Masambe would haver to control the ship to get it away, but, because of how injured they were, Keith would end up being left behind, as Maxim used the servos and the grapple to get back, Aya used the archangel suit, and her natural speed, and Harold used the stims, and just sprinted at Olympic sprinter speed all the way back).
Aya: She's just fast (Started saying she just seemed to appear, because of run and gun, and went with it).
The rest of the explanations will spoil some things with the new story. Don't read if you are going to continue:
Maxim: Is actually an incredibly powerful Psionic users, but his powers were normally kept contained by a mental barrier, which prevented the energies from overwhelming his mind and killing him, which severely limited his ability to use them. At that final battle, he forced that barrier away, and unleased his full psionic energies. Then teleporting Himself and Aya back to his apartment, before the psionic energies overwhelmed him, forcing his mind to do a last-ditch effort to protect itself, shunting him into a comma, until the psionic energies can be released without further damaging his mind.
Karl: Ran into Ryo as he was going to let the aliens in. Ryo knocked him out, and give him to the aliens. Karl then ended up being the first successful gene-engineered soldier, and became the first ADVENT officer.
Harold: Once he became aware of an attack, he had gotten his equipment, and went to the Command Deck. When he'd gotten there, they'd been attacked, and he'd been cut off from the group that got the upstairs. And, about to be overwhelmed by the aliens, he used all the stimulants his suit had on it all at once (something that the suit normally prevents it from doing), killed the nearest Berserker, ripped the claw-swords from it's hand, and used those to cut himself a path out, and charged out of the facility. He's then spent 20 years wandering around killing aliens, driven by his own rage, and a constant pain that he suffers whenever he isn't fighting something.