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The suggested order of the mission was compiled according to the following criteria:
- Escape the Laboratory
- Rescue the Reploids - Boss drops Thunder Chip
- Destroy the Train - Boss weak against Thunder Chip; unlocks mission for Flame Chip
- Occupy Factory - Boss drops Flame Chip
- Find the Shuttle - Boss weak against Flame Chip; unlocks mission for Ice Chip
- Find Hidden Base - Boss weak against Flame Chip; drops Ice Chip
- Stop the Mechaniloid!
- Rescue Colbor/Corbeau - Boss weak against Ice Chip
- Duel in the Desert - Boss weak against Thunder Chip
- Protect the Factory
- Stop the Hacking - Boss weak against Flame Chip
- Fast crystal collection from quickly regenerating spiders disappear from Underground Laboratory after completing the next mission
- Retrieve Data
- Save the Base!
- Neo Arcadia Shrine
- Neo Arcadia Tower
- Neo Arcadia Core