One characteristic of Mega Man Zero is the fact that most stages are the setting for two missions. This feature is not found in any other game in the Mega Man series and subseries.
Of course, enemies are different during the second mission in the same area; in some cases, the stage is also navigated backwards.
|Area||1st mission & boss||2nd mission & boss|
|Underground laboratoty||Mission 1 (nameless) — the Golem||Retrieve Data — Maha Ganeshariff|
|Disposal center||Mission 2 (nameless) — Aztec Falcon||Mission 7 (nameless) — the Giant Mechaniloid|
|Subway||Destroy the Train — the Train Engine||Rescue Colbor-Corbeau — Harpuia|
|Factory||Occupy Factory — the Guard Hydra||Protect the Factory — Phantom|
|Desert||Find the Shuttle — Anubis Necromancess III||Duel in the Desert — Fefnir|
|Hidden base||Find Hidden Base — Blizzack Staggroff||Stop the Hacking — Leviathan|
|Resistance base||-||Mission 13 (nameless) — Hanumachine|
|Neo Arcadia Shrine||Neo Arcadia Shrine — Herculious Anchortus||-|
|Neo Arcadia Tower||Neo Arcadia Tower — the Rainbow Devil||-|
|Neo Arcadia Core||Neo Arcadia Core — Copy X||-|
The suggested order of the mission was compiled according to the following criteria:
- Mission 1 - the Golem
- Mission 2 - Aztec Falcon: Boss drops Thunder Chip
- 12. Retrieve Data - Maha Ganeshariff: in Jackson Mode and Ultimate (Easy) Mode, obtain the weapons earlier.
- Destroy the Train - the train engine: Boss weak against Thunder Chip; unlocks mission for Flame Chip
- Occupy Factory - the hydra guardian: Boss drops Flame Chip
- Find the Shuttle - Anubis Necromancess III: Boss weak against Flame Chip; unlocks mission for Ice Chip
- Find Hidden Base - Blizzack Staggroff: Boss weak against Flame Chip; drops Ice Chip
- Mission 7 - the giant mechaniloid: (Stage 2 revisited)
- Rescue Colbor-Corbeau - Harpuia: Stage 3 revisited; boss weak against Ice Chip
- Protect the Factory - Phantom: Stage 4 revisited
- Duel in the Desert - Fefnir: Stage 5 revisited
- Stop the Hacking - Leviathan: Stage 6 revisited
- Retrieve Data - Maha Ganeshariff: Fast crystal collection from quickly regenerating spiders disappears from Underground Laboratory after completing this mission.