The game takes place two months after the events of Mega Man Zero 2 and follows series protagonist Zero as he attempts to stop a new villain, Dr. Weil, from wreaking havoc on Neo Arcadia.

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.

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.

Dr. Weil reveals he has resurrected Copy X, who resumes his rule over Neo Arcadia, much to Harpuia's chagrin.

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.

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.

Omega's death results in a massive explosion, which frees the Dark Elf from Dr. Weil's corruption, However, Harpuia, Fefnir, and Leviathan's fate is unknown due to different sources stating that they survived while others say they perished.

When charged up, a powerful stabbing attack is performed, which can knock enemies back, or propel Zero into the air if aimed down to the ground, like a makeshift pogo stick.

It is said by one Resistance Member (Hirondelle) that the portal to Cyberspace opened up due to Omega's arrival.

These Chips give direct upgrades to Zero's head, body or legs, and can be used to reproduce the effects of the various Forms that Zero could take in Mega Man Zero 2.

In Hard Mode, Cyber Elves cannot be used and Cyberspace cannot be accessed (save for one specific level).

[4][5] Mega Man Zero 3 was the fourth best-selling video game in Japan during its week of release.

A common comment made by reviews of the game is that Mega Man Zero 3 is similar to its predecessors and has not changed much in terms of gameplay.