Oppressed humans begin to escape in large numbers to the last-known livable location on the planet, Area Zero, prompting violent retribution from Neo Arcadia.

[4] Since its original release, it has been brought to the Nintendo DS family of systems as part of the Mega Man Zero Collection in 2010 and the Wii U's Virtual Console in 2016.

In February 2020, it was released on PC (Steam), Nintendo Switch, PlayStation 4, and Xbox One as part of the Mega Man Zero/ZX Legacy Collection.

[5] Cyber Elves, a core element of previous Mega Man Zero installments, are small helpers who can assist Zero in combat.

In addition to this, Zero can now equip body chips to enhance his abilities, including double-jumping and self-recovery, similar to early Mega Man X titles.

Neige explains they were en route to Area Zero, the crash site of the space colony Eurasia, which has become one of the last places on Earth that can support human life.

[13] Shortly after parting ways, Zero learns of a plot called "Operation Ragnarok", meant to destroy all environments outside of Neo Arcadia in order to force humans to return and live under Dr. Weil's rule.

After Zero eliminates the remaining Einherjar Warriors, Ciel intercepts a radio message from Dr. Weil, who reveals that Operation Ragnarok was a ruse.

Dr. Weil reveals that, while he is human, his mind was transplanted into a constantly-regenerating mechanical body by the people who exiled him at the end of the Elf Wars, rendering him effectively immortal.

[18] Believing he can survive the impact of the crash and personally oversee the destruction of Area Zero, Dr. Weil fuses himself with Ragnarok's power core and attacks Zero.

Zero chooses to stay on Ragnarok as it plummets into Earth's atmosphere and defeats Weil again, destroying the station utterly and neutralizing the threat of its crash.

[19] Heartbroken, Ciel runs off alone and breaks down in tears, promising to carry on Zero's mission of maintaining peace between humans and Reploids.

[23] Mega Man Zero 4 has an average of 77% on Metacritic and GameRankings, making it roughly the 92nd best-ranking Game Boy Advance title.

[30] According to Media Create sales information, Mega Man Zero 4 was the 177th best-selling video game in Japan in 2005 at approximately 74,354 copies.

[31] Mega Man Zero 4 has been called a "refined version of an outstanding platformer series"[7] with a more streamlined weapon and Cyber Elf system.