Walkthrough
When you arrive to the Clock Tower, you will discover R being held in a massive quantity within a bomb that is set to go off at any minute. Emilia will attempt to go Find Mr. Holiday, leaving Tim and Pikachu to have to dismantle the large machine and then disarm the bomb containing R. All of this will be done by Fast Action Events, so be prepared to make some quick moves on the fly.
After preventing the bomb from going off and thus dispersing the last known bit of R, Tim and Pikachu will have to think about their adventure thus far in order to determine who is the true mastermind behind the situation with R. Before long, the two will realize that only Keith knew that Pikachu couldn't use attacks, yet somehow Roger referenced this just shortly ago. Clearly, Roger had been behind the production of R all along!
Just when the duo figures this out, Roger arrives with Emilia as his hostage, having caught her trying to leave the Clock Tower in order to get help. Realizing his plan has failed, he will attempt to still spread R using the fail safe, the same he had installed in Case something like this happened. Using Emilia as his hostage to his advantage, Roger will try to force Tim to turn on the valves for said machine. Having no other choice, Tim will begin to do so. However, as he does, Tim will slowly stall, allow Pikachu to disappear out of sight. After being distracted for long enough, Pikachu will jump down from above at Roger.
Just then, Roger will call upon Keith's Noivern for assistance. Roger is using the new and improved version of R on Noivern, giving him absolute control of all the Pokemon's actions. He will force Noivern to Attack, and as it does, Pikachu will somehow finally be able to use a Thunderbolt. You will be sent into your final Fast Action Event of the game, needing to prevail in order for Pikachu's Thunderbolt to stop both Roger and Noivern. Once Pikachu has stopped the two of them, your final Case will End and the Epilogue will begin.
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Who Is The True Culprit: Use all of the information you have gained up to this point to determine who is the real mastermind behind unleashing R!
Disarm The R Machine: Rapidly click the A Button to remove the first plug. From there, press the Red Button and remember the colors that follow, as you must press the buttons in the correct order as shown.
Stop Roger: Rapidly click the A Button to help push Pikachu's Thunderbolt towards Noivern.