Originally thought to be Aplodia Neuro, her true identity is that of Code Amelias, the descendant of The Old Generation System. She tried to seize both of the Generation Systems and replace Aplodia's existence, becoming the ruler of the world.
At an unknown point in time, the GNC-666 Balbadoro stole the code containing Amelias's identity and powers. With the mobile fortress en route to the Generation System, Amelias is forced to fight in the GGH-001C Halphas Böse to regain her identity.
Amelias has access to a code labelled by the other original characters as "Betrayal," which, when executed, causes Earth's Generation System to malfunction and drive those under its influence to violent levels of insanity. This was initially used to subvert Setsuna F. Seiei's attempt to communicate with the ELS and use the other four pilots who had joined him as a firing squad of sorts to try and murder him on the spot, as Amelias saw him as a liability to her mission. This fails, and the pilots are subsequently freed, though the ELS would go on to harass the Jupiter Empire and assimilate Libra in later stages.
Amelias spends the EX stages of Overworld posing as Aplodia to deceive the player into helping her regain her identity. Her presence, combined with the Generation System and various catastrophic events, causes a civil war between the antagonists of the Gundam multiverse. Interestingly, Ribbons Almark calls Amelias a "phantom" who deceived humanity with the World Signal, hinting at her true agenda.
After much strife, Amelias catches up to Balbadoro, which is now ready to crash into Earth, presumably to destroy the Generation System, and summons the Halberd, transforming the Halphas Bose into the Halphas Bose Halberd. As a result of Balbadoro stealing Amelias's powers, it turns her Betrayal code against her, slowly but surely turning the team sent to stop it against each other. Regardless, after the player shoots down Balbadoro, Amelias charges after Balbadoro, destroying the Neuro army sent to protect it, and purges the Halberd to seize it personally. Although Balbadoro manages to grab the Halphas Bose with its large claws, Amelias draws a dagger from its wrist and impales Balbadoro's head with it, causing it to explode and burn up in the atmosphere.
With her identity regained, Amelias attempts to take over the world. Code Amelias is later found in a basement in the old Generation System by Aplodia Neuro and Code Phoenix, launching her invasion army and activating the GS-A0 Queen Amelias. When Code Phoenix attempts to stop her alone, Amelias executes Over Impact and he is forced to fight Aplodia , although Phoenix eventually regains his senses. Combining forces of the player's, Aplodia and Phoenix, Amelias is utterly defeated by the overwhelming power. To punish her for her sins, Aplodia de-powers Amelias, turning her into a fearful little girl who eventually becomes deeply homesick. Upon learning that the old Generation System is ready to destroy Earth, Amelias's fear also drives her to protect the planet out of instinct. Due to this, Amelias tries to return to the old Generation System, requiring Phoenix's intervention due to the extreme danger involved, and what appears to be the System's desire to destroy Earth.
Hidden Past - Is this my home?
Amelias and Code Phoenix eventually reach the "mother" of the old Generation System - First Aplodia. Then he discovers that the computer requires Amelias to reboot the system. It initially seems too late for Phoenix as the computer lured Amelias by posing as her home. The various chambers of the system begin to activate security protocols of increasingly freakish nature - first materializing the mobile suits of the Gundam antagonists allied with the player during the EX stages with Neuros impersonating their pilots (with nukes providing some semblance of cover fire), then conjuring mobile armors and possibly a full-size Devil Gundam, and finally transmuting statues of the Gundams of the protagonists of each featured series into their real counterparts, also controlled by Neuros impersonating their pilots. As Code Phoenix reaches the center of the old Generation System, the core assimilates Amelias, and attempts to materialize its last trump card - the GGV-000 Barbatos Mirage. Regardless, the player's overwhelming power easily crushes it, and Amelias is freed after the system shuts off.
Epilogue - I'm home,mom.
After Amelias awakes, Code Phoenix informs her that he has "took care of everything" and is ready to prepare a (new) home for her. The two return to the new Generation System on Earth, and Phoenix uses his code to encase the Earth in a protective shell, preventing future crises from ever occurring.
She seems to be inspired in Werbellia The Swamp Witch from the Queen's Blade franchise, including sharing the same voice actress. This is also possibly reinforced due of the name of her Mobile Suit and her background.