Walkthrough
With Roger finally defeated and apprehended, and the Case of about R now having come to its close, Mewtwo will appear once more. Pikachu will return the final Cells used to create the Substance known as R to Mewtwo, fulfilling the promise he made to it not so long ago. After Pikachu does, Mewtwo will remind Pikachu of the mysterious choice it gave it to make, the same it must now decide upon. Pikachu will tell Mewtwo that its choice is easy to make, fainting almost immediately after saying this.
Tim will confront Mewtwo after this happens, but Mewtwo will assure Tim that it didn't harm Pikachu, that his partner is only asleep. From there, Mewtwo will share some information with Tim, the same information (though not to the fullest extent) that Tim has been looking for since his adventure with Pikachu first began. Mewtwo will tell Tim that his father is still indeed alive, and that Tim should be able to Find him if he doesn't give up hope. Mewtwo will then depart, with Tim taking Pikachu and leaving as well.
The following day, Tim will wake up to Find Pikachu not acting like he usually does. Instead, Pikachu is acting like that of a normal Pikachu, unable to talk with Tim as before. At first, it appears this effect is permanent, that this could possibly be the choice that Mewtwo forced Pikachu to make. However, in the end, it turns out that it was all a bluff on Pikachu's part, that is can indeed still communicate with Tim. Pikachu, as the game comes to its conclusion, assures Tim that he will be his partner for a while, beginning with the next step of locating his father, Harry Goodman.
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