Darkrai

Introduction
Darkrai was  Mewtwo's  faithful general from the beginning, but when Mewtwo turned bad (for unknown reasons) and started working on the Hydra Project, Darkrai opposed him. Mewtwo then possessed Darkrai and made him a partner to the evil project.

Season 2
Darkrai first appeared at the end of Season 2 as he started the Hydra Project in the mysterious cabin.

Between the Seasons
Darkrai took a small part between Seasons 3 and 4. After Deoxys was tefeated by Team Leaf Blade and AKD, Darkrai took Deoxys in and "resurrected" him (all on Mewtwo's orders, of course).

Before Deoxys took Darkrai's place in controlling Lucario, Lucario took advantage of the weak control of a non psychic type Pokemon and went to destroy the cabin. Darkrai immediately got to the scene and transported the fetus Hydra to the Crystal Cave, Mewtwo's old base.