Original: During the course of the game, Samus works to prevent the Phazon from spreading from planet to planet while being slowly corrupted by the Phazon herself.
Simplified: A month later, Samus finds out that Dark Samus' Phazon (like poison in our world but worse) based attacks have corrupted her. She (along with the rest of the bounty hunters) is fitted with a Phazon Enhancement Device (PED) which allows her to use the Phazon within her.