Mega Man Zero 3 [a] is a video game developed by Inti Creates and published by Capcom for the Game Boy Advance (GBA) handheld game console. It is the third video game in the Mega Man Zero series of Mega Man video games. The European version featured a completely different logo, which was also used on Mega Man X7 , Mega Man X8 , Mega Man X: Command Mission , Mega Man Zero 2 , Mega Man Zero 4 , Mega Man Network Transmission , Mega Man Battle Chip Challenge , Mega Man Battle Network 3 , Mega Man Battle Network 4 , and Mega Man Battle Network 5 . In February 2020, the game was released on the PlayStation 4, Xbox One, Nintendo Switch, and PC via Steam as part of the Mega Man Zero/ZX Legacy Collection .

Two months following Zero's victory over Elpizo, the Dark Elf remains at large. During this time, Ciel has finished her research on a new energy supply to end the crisis, dubbed the "Ciel System". While en route to Neo Arcadia to propose the Ciel System in hopes of ending the conflict and the genocide of Reploids, a spaceship with the Dark Elf's energy reading crashes to Earth.

Zero sets out to investigate, but instead finds the remaining Guardians (Harpuia, Fefnir, and Leviathan) fighting against a gigantic Reploid named Omega and a scientist named Dr. Weil — both who were banished to space due to their crimes in instigating the Elf Wars and turning the Mother Elf into the Dark Elf a century prior. Dr. Weil reveals he has resurrected Copy X, who resumes his rule over Neo Arcadia, much to Harpuia's chagrin. The Guardians, suspecting that Copy X is being heavily influenced by Dr. Weil, defect from Neo Arcadia. Zero and Dr. Weil go their separate ways in search of the Dark Elf.

The Dark Elf appears in a human residential district in Neo Arcadia, leading Dr. Weil and Copy X to launch a missile in order to incapacitate it. Although successful in capturing the Dark Elf, the incident kills thousands of humans. Following this event, Ciel rescinds her offer of the Ciel System, leading Dr. Weil and Copy X to brand the Resistance as Mavericks and subsequently launch an invasion against them. The Resistance is able to delay the invasion until Zero locates Copy X. During the ensuing battle, Copy X is betrayed and killed by Dr. Weil, who declares himself the new ruler of Neo Arcadia and announces his true intention for capturing the Dark Elf: to fuse it with Omega and link them with a frequency transmitter that would enable Omega to control the minds of every Reploid on Earth.

Zero confronts and defeats Omega, who reveals his true form: a body that looks exactly like Zero. Dr. Weil reveals that while Zero was powered down during his 100-year hibernation, he had transferred Zero's conscience and memories to a copy body and stole Zero's original body to be used by Omega due to its unmatched fighting abilities. Despite this revelation, Zero and the Guardians destroy his original body, killing Omega for good. Omega's death results in a massive explosion, which frees the Dark Elf from Dr. Weil's corruption, but kills Harpuia, Fefnir and Leviathan.

While Zero is unconscious, X appears and tells Zero that it's up to him to protect the Earth and defeat Dr. Weil. Finally out of power, X vanishes forever. The Dark Elf, known as the Mother Elf once more, delivers Zero to the Resistance Base before flying away.

Starsgame has programmed and prepared this game for smartphones (Android operating system).