While Hope had left from the group, they noticed the journal of Team Lyoko adventures pages vanishing again, thinking it is Flux, they waste no time heading back into the past. But unknown to them there, it was all the work of a new but familiar threat: Nebula. Now led by Cosmo Man, they seeked to destroy the heroes from the inside.
Over the course of their time, they learn Volts identity as a Skyian, Twilight had been summoned to the Dive to the Heart along side Toma, and a third boy who was revealed to be Sora later on, both sora and Twilight chosen by the keyblade, and Toma who wields the Shining Force venture through the area before approaching a large shadowing creature. They battled it fiercely before finishing it off. It was then that the experience in the area ended as Twilight awoke in a strange world with Gajeel and Pantherlily, both explaining they were warped here by Clock Man.
Back on Kadic, dealing with pressuring items to get in their way of a double life on Lyoko, the warriors begin talking about bringing on a new member to the team. They consider William but Yumi rejects the idea due to her feelings towards him. But even though this was going on, she couldn't deny the help. XANA was desperately attacking Sector 5. The Scyphozoa was also on the job, Hitting Aelita and forcing her to enter Code: XANA, destroying one sector at a time, to get rid of any chance for the warriors to fight him. And even while this happened, the members of Nebula continued to send their forces after them, but for mysterious reasons, they all kept being disabled one at a time, under the notion that there was a traitor among them.
The Warriors finally decide to put William on the Lyoko Job, just as Hope comes back with a team of his own. He explains what he’s learned of the traitor and introduces his Squad, consisting of Gemini, Erica, Ceil, Nana, Alisa, Espio, Charmy, Aang, Sokka, Katara and Toph in addition to Fuyunyan and Hsien-Ko. But the last member was a surprise, the larger-than life and the first of many beings known as enhanced: Titanica.
A little after this happened, Cosmo Man was growing impatient and even resorted to beating Ulala, who he had taken captive during their plans. It was then that the true identity of the killer made themselves known. Standing before them was the same weapon that Nebula had taken for their uses. Project B, better known as...Bass. Bass fought Cosmo Man and won, disbanding Nebula through his beliefs of teams being a sign of weakness and that your own power is the true form. After which, he allowed Ulala to leave and went to a jack port in order to meet the Lyoko Warriors head on as well as look for a worthy opponent.
With all Sectors gone and the Warriors in testing, XANA attacks Sector 5 once more, William and Aelita being the only ones to respond. Bass enters the fray, but so does Yang, realizing what Hope meant about the group pushing themselves. She goes to lyoko with her new arm in order to fight on her own. SHe and Bass then enter a gruesome fight to the death, neither of them giving an inch. Meanwhile, it was too late for william. Getting cocky and facing the Scyphozoa all on his own, the dreaded monster infects him with XANA’s programming, putting him under XANA’s control. He proves himself powerful defeating the Lyoko Warriors with ease and destroying the core as well as all of Lyoko. It was all gone. After this, the group left defeated with Yang gaining a rival in the process. They now set out on a new mission: defend the Classic Yo-kai and defeat the Kaima.