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>Team Rocket and its HQ is the only villainous team still active
How awesome would it be if they introduced Silver into the anime as Giovanni's son? He'd be a serious trainer conflicted with the current state of Team Rocket. Prior to this, though, Giovanni would be on the verge of finishing the completion of his Pokemon Army... all they need to do now is stop Team Flare, who are also on the verge of utilizing their Death Cannon. All out war between the two forces would occur with Ash and friends caught in the middle. All the past Rocket Grunts would make appearances including Biff and Cassidy, Pierce, Zager, etc...
The TRIo would be conflicted with how to honestly handle the son of da Boss. At the end of this war, Team Flare is defeated and Team Rocket has taken ~severe~ casualties. That, however, would not stop Giovanni from attempting to renew his forces, being the only evil Team left. Silver would be branded a traitor to Team Rocket during the war and would proceed to Rocket HQ to put an end to his father's ambitions once and for all before he is able to renew his forces.
Intense battles transpire as Ash, Silver and the rest climb the massive Rocket HQ floor after floor. Ultimately, only Ash and Silver make it to the top, the others on lower floors holding back reinforcements. One massive door is all that's left between them and Giovanni, guarded by Jesse, James and Meowth. As Ash prepares his Pokeball, Jesse holds puts up her hand saying there's no need for a battle. The TRIo then go into a speech about how they've been happy to serve under Team Rocket all these years but now they know this is the end... they leave their posts and walk past Ash and Silver. As they're doing so, James puts his hand on Ash's shoulder and, without making eye contact, apologizes for all the trouble they've caused him over the years.
Now, with nothing left in their way, Ash and Silver push through the final door.
