There's a reason most roleplaying games don't generally allow a single player to play multiple characters, and there's an even better reason they don't generally allow playing characters on opposite sides of a conflict. Things can get kind of convoluted.

During the events of a game, it can happen that characters change outlooks and allegiances. Examples include when heroes become corrupted by events or forces beyond their control, and descend into decadence and evil, or become pawns of a greater power. Many a hero has fallen victim to a vampire and become a thrall of the villain, or been compromised under similar circumstances. The general approach is to retire the character as a player character and have the GM take over as an NPC, leaving the player to pick up a new heroic character.

But you don't have to do things that way. You could have a player play a villain behind the scenes. Just be prepared for the out-of-character weirdness that can result.

Transcript

General Veers: Lord Vader, this is farcical. I'm riding in a giant attack camel.
Darth Vader: {hologram} Is it working?
General Veers: Well... yes.
Darth Vader: Then I shall land my troops.
[SFX]: Pow!
Luke: Princess! I think they're going to start landing troops soon.
Leia: Are you sure? We're not picking up any landers.
Luke: I've just got this feeling.
[SFX]: Pow!
[SFX]: Pow!
R2-D2: Annie, you're actually playing the leaders of both sides of this battle. Can't you at least arrange for us to be attacked by a fleet of hyperdreadnoughts as well?
[SFX]: Pow!
Leia: You want the Rebels to be annihilated?
Chewbacca: He just wants a hyperdreadnought.
[SFX]: Kaboom!!