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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
Final stages
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 -

Another characteristic is that when you clear one stage, one or more new stages are unlocked, in a fashion similar to Mega Man & Bass. This feature was lost in the subsequent Mega Man Zero games.

The graphics from Mega Man & Bass were chosen to highlight the similarity.

Suggested order[edit]

The suggested order of the mission was compiled according to the following criteria:

  1. Mission 1 - the Golem
  2. Mission 2 - Aztec Falcon: Boss drops Thunder Chip
  3. Destroy the Train - the train engine: Boss weak against Thunder Chip; unlocks mission for Flame Chip
  4. Occupy Factory - the hydra guardian: Boss drops Flame Chip
  5. Find the Shuttle - Anubis Necromancess III: Boss weak against Flame Chip; unlocks mission for Ice Chip
  6. Find Hidden Base - Blizzack Staggroff: Boss weak against Flame Chip; drops Ice Chip
  7. Mission 7 - the giant mechaniloid: (Stage 2 revisited)
  8. Rescue Colbor-Corbeau - Harpuia: Stage 3 revisited; boss weak against Ice Chip
  9. Protect the Factory - Phantom: Stage 4 revisited
  10. Duel in the Desert - Fefnir: Stage 5 revisited
  11. Stop the Hacking - Leviathan: Stage 6 revisited
  12. Retrieve Data - Maha Ganeshariff: Fast crystal collection from quickly regenerating spiders disappears from Underground Laboratory after completing this mission.