Here's how it happens:
* In the anime: Medusa is killed by Maka Albarn and Soul Eater Evans in a climactic battle in the DWMA headquarters. Her death is a pivotal moment in the series.
* In the manga: Medusa's death is a bit more complex. She survives her initial battle with Maka and Soul, even managing to escape with her son, Crona. However, in the final battle, she is fatally wounded by Asura, the true antagonist, and ultimately dies in Crona's arms.
Note: The anime adaptation of Soul Eater deviates from the manga in some details, including the circumstances surrounding Medusa's death.