Although there is nothing wrong with the Transfer System, Bill quickly realizes something and heads to the Pokémon League's control room. He begins investigating the Transfer System, but Daisy Oak notes that he is injured after protecting her from the debris. Bill tells her that it's alright since the Gym Leaders are also doing their best to help. Daisy helps Bill move a large monitor away from the keyboard and states that she wants to help everyone as well. Bill notes that although he suspected the Transporter broke down because of a hacker, he hasn't found any proof yet. Bill notes that hackers can do more than just tamper with the systems. Bill manages to figure out that the machine hasn't been tampered with, but the screen showing how much energy it has was altered to make it look almost full when it is actually completely empty.
Bill begins looking for a source of energy to move to the Transfer System, but the damage done to the League left everything without power. Furious, Bill begins blaming himself for being unable to answer the wishes of the people who sent the faxes. Daisy quickly points out that one of the train cars has a constantly increasing large amount of energy inside of it, which was left behind by Lt. Surge's Raikou. Bill immediately calls Hiro and tells him to inform everyone that the Transfer System is fixed. Hiro uses the Radio to tell everyone all around Johto and Kanto that the Pokémon Transfer System is now fixed and they can send in their Pokémon to the Ilex Forest to help.
The Pokémon Fan Club Chairman tells fellow Pokémon lovers around the region to listen to what Hiro said and send in their Pokémon to help. With the push of a button, Bill restarts the Transfer System, which is now being filled with several Pokémon. In Azalea Town, several Pokémon rush out of the Pokémon Center and into the battle.
In Ilex Forest, Green struggles to hang on to Moltres. She loses her grip and goes flying, but is saved at the last second by Blue. Red notes that if they can get closer to Ho-Oh and Lugia, they would have a better chance at succeeding. However, Ho-Oh and Lugia's attacks make it impossible for the three to get any closer.
They note that Legendary Pokémon would never work with someone like the Masked Man, so it's up to them to free them from his control. Red tries to think of a way to save them but notices a large cluster approaching from afar. The group is revealed to be the Pokémon that exited the Azalea Pokémon Center. The Pokémon begin grouping around Ho-Oh and Lugia, each sharing the thoughts of stopping evil with their Trainers. Together, the combined efforts of the Pokémon allow Ho-Oh and Lugia to be freed from the Masked Man's control. Now freed, Ho-Oh and Lugia nod at each other and take to the skies. With Ho-Oh and Lugia gone, the three are free to move to the Ilex Forest shrine. Red asks Green if she can return, Moltres, Articuno, and Zapdos to their Poké Balls. Red states that for the final battle, they should use their starter Pokémon. Red returns Blasty and Charizard. The three send out their Pokémon and head towards the shrine.
Will, having seen the amount of Pokémon gathered along with Ho-Oh and Lugia's release, decides to make his escape. A voice appears and tells Will that he's forbidden to run away. Elsewhere, Raikou, Entei, and Suicune head towards the forest. The voice is revealed to be Pryce, who states that Gold had kept chasing him, but he managed to get rid of him for the moment. Pryce steps on Will and demands to know why he has not kept people from coming near the shrine. Pryce notices that he is surrounded and tells everyone to come out from behind the bushes.
Silver and his Feraligatr jump out from the bushes with Green, Red, and Blue also coming out. Green tells Pryce that they freed Ho-Oh and Lugia from his control. Crystal arrives with Suicune, Entei, and Raikou. Yellow exits from the bushes, much to Red and Crystal's surprise. Exbo comes out as well, with Pika and Chuchu on his back. Silver tells Pryce that his ambitions will be stopped and commands the six Pokédex holders to attack the villain. While this happens, Crystal wonders where Gold is.