| Spoiler warning!|
This article contains plot details about Pokémon Fusion Generation.
Ellie's appearance is indistinguishable from any other female Team Magma grunt for most of the game, before she cuts ties with Team Magma following their hijacking of the Magnet Train. Unlike the rest of Team Magma she doesn't seem to care much about Team Aqua and Team Magmas' ultimate goals, their leader, or Pokémon Fusions. Ellie is naive, thinking that her teammates are her friends, even though they mistreat her and abandoned her in Rock Tunnel. She is also shown to be forgetful and not very bright. Upon meeting Brendan/May, she warns them about someone matching his/her description perfectly, and upon meeting them a second time is unable to remember them at first (though these incidents could be attributed to Ellie spending a long time in the darkness of Rock Tunnel).
Prior to the events of Fusion Generation, Ellie lived with her mother and sister Mira in Celadon City. When her sister died, their mother moved to Ecruteak City and Ellie, unable to cope with her death, left to join Team Magma.
In Fusion GenerationEditEllie is first encountered in Rock Tunnel where she has been wandering around in the dark until Brendan/May found her. She joins the party and helps in battle with her Golbat. She passes on a warning from her teammates to Brendan about "a boy wearing a white hat" or to May about "a girl in red." When they finally make it through the cave and catch up to Team Aqua and Team Magma, an Aqua grunt scolds her for unwittingly partnering with the enemy they warned her about. She rejoins them, but returns briefly to thank Brendan/May and give them the Itemfinder.
The player encounters Ellie again on the Magnet Train while in disguise as a Magma grunt. Ellie can't place them at first, but eventually recognizes them and blows their cover. After being reminded of Team Aqua and Team Magma's objective, Ellie apologizes and a battle ensues. By this point, she has acquired her own Pokémon Fusion, an Igglybat.
After Brendan/May defeats Team Aqua, Team Magma, and Marco, they threaten to detonate Electrode. Ellie, in a moment of clarity, realizes the seriousness of the situation and urges them not to. She quickly loses focus though and indirectly causes Electrode to explode.Ellie survives the explosion under New Bark Town and heads back to the Kanto region. Along the way she encounters Blue, who berates her for her role in the explosion and the failure of his escape plan. Consequently, she decides to leave Team Magma. She later runs into Brendan/May, who initially doesn't recognize her without her uniform, and apologizes for her actions. She says she would like to remain friends, admitting she's never really had any others.
After defeating the Elite Four, Ellie is seen in Ecruteak City entering the home of Mira's mother. Inside, they reunite and it's revealed that Mira was Ellie's sister. Ellie thanks the player and rewards them with Igglybat.