Mewtwo vs. Genesect Army Subplot
Not too long after Cheren and Accel return to Unova and Touya returns from Hoenn, Mewtwo shows up at the P2 Laboratory, which is still active. They still have the containers for the Genesect when they were creating them and it triggers bad memories for Mewtwo. So, he blows it up and flees for the mainland.
Touya first catches a glimps of Mewtwo over Striaton City. When he realizes what it is, he calls Red and Green while on his way to catch up with Cheren about the Genesect Army.
Mewtwo travels around, from cave to cave, finding people or pokemon there when he just wants to be alone. Eventually, he ends up in Chargestone Cave and encounters a group of metal pokemon. One of them is a shiny red. Using his psychic abilities, he reads into them and tries to emphaize with them since they were both human made but the red leader rejects him and attacks. The rest of the genesect follow suit, and Mewtwo fights them off until he can get away from them.
Cheren is too late when he shows up at Chagestone Cave after getting the signal from Sird’s device and hearing reports from bystanders, but along the way, he picks up Shaymin and tells Hikari he has her.
Touya finally encounters the genesect army near Lostlorn forest. After yet another misunderstanding, they try to fight him off, then flee. Touya tries to get a hold of Cheren, but because Shaymin is freaking out to Hikari about what it’s like going through the rings, Cheren misses Touya’s texts and calls.
Turns out, the army did not flee too far. Mewtwo is annoyed, so he starts fighting back the next time they clash - which is in Black City. The same Black City Madame Boss currently resides in.
Touya is the first person on the scene and confirms with Red and Green where to meet him. Cheren also arrives after giving Shaymin to Hikari. The whole scene is a complete mess, with citizens fleeing in the wake of the fighting pokemon. It only gets worse when Madame Boss officially enters the fray.
The kids split up: Red and Green try to break up the now one-on-one match between Mewtwo and the Red Genesect, while Cheren and Touya are trying to keep Madame Boss from capturing the other Genesect. Accel is let out of his pokeball to try and protect them and calm them down.
Madame Boss also has her grunts, which makes the situation “A Complete Bother”. But Red and green take down the ones who are after the Red Genesect, and Touya and Cheren are able to take down the other grunts with no problem.
The Red Genesect still is able to control the minds of the other genesect to the point of having them attack all humans. Even while fighting Mewtwo (who the Red Genesect thinks is on the side of the humans), he has a vague hold on them.
Touya gives an inspirational talk to try and snap the genesect out of it, and it almost works, but it isn’t enough. What helps them snap out of it is when they see Accel protect Cheren and Touya from an attack. The Red Genesect asks Accel why would he protect these humans, and Accel explains that it’s because they’re his friends. It causes the Red Genesect to release its hold on the other members, having them regan their own free will to do what they want.
Madame Boss almost uses this as a chance to catch one of the Genesect Army members, but Accel’s hyperdrive mode is activated from reaching such a low HP level. They defeat Madame Boss.
The officers in the city manage to arrive and arrest her, but she doesn’t leave quietly. The whole time, she tries to guilt trip them for beating her.
Cheren talks to the Genesect army about coming with him and providing them with a “home”. Meanwhile, Mewtwo managed to slip away, but Red and Green goes after him and follow him to the city outskirts. Before Mewtwo can leave, they end up having to battle him to get him to listen to their plan of bringing him back to Kanto, and that they just want to him, only for him to get sucked into a hoopa ring.
