Two members of Team Rocket, Jessie and James, are being controlled by Mewthree and therefore are currently not working for Giovanni. Jessie and James work by taking Rare Candy and hypnotizing people with their Drowzee. Jessie and James seem to work under Brock, who is also under Mewthree's control.
Player and Joey
During the story, the player character and Joey discover that Team Rocket intends to aid against Mewthree and decide to join them. The player's initiation into Team Rocket makes up the Lavender Town level's plot.
Giovanni acts as the leader of Team Rocket. In Lavender Town, he reveals the method to break Mewthree's mind control and administers the player's initiation test with his Persian.
The talking Meowth appears in Saffron City claims to be in charge of "Human to Pokemon Communication." During the level, the player must protect Meowth and prevent him from being abducted by the invading Pokemon. Meowth also confirms to have been partnered with Jessie and James before Mewthree got to them.