The game is set 100 years after the events of the Mega Man X series and follows Zero, a Reploid awakened from his sleep to aid a human scientist named Ciel and her resistance force in a fight against the utopia of Neo Arcadia.

Mega Man Zero was produced as a commission product by Inti Creates for Capcom, who were given free rein on the project's direction and premise.

The initial idea for the antagonist was to have the original X be the villain, however this was changed late into production to a copy robot due to fears of it not sitting well with players.

Critics praised the game's storyline, graphics, and tweaks to the franchise's classic action formula, though many were put off by its high difficulty level.

Ciel, desperately seeking his help, explains they live in a world where Reploids are incorrectly accused of being Mavericks and systematically "retired", apparently under the direction of the once-famed X.

[8] Shocked at this revelation and filled with doubt about his own identity as the Maverick Hunter of legend, Zero helps Ciel escape and joins her Resistance to fight against X and the utopia known as Neo Arcadia.

[9] Zero conducts missions on behalf of the Resistance in order to buy Ciel time to create a new energy source that will provide everyone with a safe place to live.

In the midst of the chaos, Ciel confesses to Zero that she helped create Neo Arcadia as a utopia where humans and Reploids were finally able to live in peace with X as their leader, but her plans fell apart when an energy shortage crisis began and X mysteriously disappeared.

[11] Zero invades Neo Arcadia and battles his way through the Four Guardians: Sage Harpuia, Hidden Phantom, Fighting Fefnir and Fairy Leviathan.

As in the Mega Man X games, the player can dash along the ground, cling to and scale walls, or perform a combination of these abilities.

[4][7] Unlike previous titles in the franchise where separate stages are selectable from a menu, Mega Man Zero is presented as a single, interconnected overworld.

[6][15] Up to three Cyber Elves can be equipped for a given level and some can only be activated once they are fed sufficient energy crystals picked up or collected from defeated enemies.

[18] The game was produced by Inti Creates president Takuya Aiza and was co-directed by Ryota Ito and Capcom's Yoshinori Kawano.

[15] Though Zero was mostly depicted as a benevolent hero in the X series, the designers wanted to blur the line between good and evil when drawing up the new game's narrative.

[15] The game's main antagonist was a popular topic of discussion during production, and the developer often sought input from Capcom in this regard.

According to Ito, Inti Creates realized that it "wouldn't sit so well with the young boys and girls that really do see [X] as a hero", so they replaced him with Copy X just one month before release.

Next, as Nakayama found it difficult to design the Cyber Elves, they were represented as simple balls of light or incomplete portraits within the game.

[22] Yamada wanted to differentiate the style of music of the Mega Man Zero series from this predecessor by treating it "more like a television or film-like presentation than the stage system like before".

[22] In addition to the 21 songs, this CD features five drama tracks; commentary tracks by Yamada; an interview with the Inti Creates sound team; character descriptions and an interview with character designer Toru Nakayama; and guest liner notes from artist and manga creator Hitoshi Ariga.

[35][36] The game would also be re-released in 2020 as part of the Mega Man Zero/ZX Legacy Collection for PlayStation 4, Xbox One, Nintendo Switch and PC; the compilation includes the original Japanese version, complete with the blood, which resulted in a T for Teen rating.

[37] Mega Man Zero has met with a mostly positive critical reception, holding scores of 81% and 82 out of 100 respectively on the aggregate review sites GameRankings and Metacritic.

A manga based on the series was written and illustrated by Hideto Kajima and serialized in the monthly Shogakukan magazine CoroCoro Comic from June 2003 to February 2006.

[57][58][59] An art book titled Mega Man Zero Official Complete Works was published in Japan by Capcom in 2006 and in North America by Udon Entertainment in 2008.

[60][61] The book contains detailed information on the series, promotional artwork, concept designs and sketches, and interviews with the Inti Creates staff.