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Unlike other modes which start at a random Star system, this mode provides a series of events that start at a fixed point in the universe. It is split into six phases with eight milestones in each one. Achieving each milestone results in substantial rewards in the form of Expedition Patches, Items, Blueprints, Exosuit and Starship slots, and even a new S-class starship, Honmatan OQ5 (33+21 slots), and a new S-class Multi-tool, Geometric Dream Inverter.
Similar to other game modes, players start away from their starship and need to reach and repair it. However, Hermetic Seal and Portable Refiner blueprints are already known.
The starting Multi-tool in Expedition mode is called Trace of Zeal, has a larger number of slots (12) and is equipped with the following features:
A random weapon
X-Class Mining Beam Upgrade Module.
The Exosuit is initially equipped with two random upgrades to either Jetpack, Life Support, or Hazard Protection systems, and has 27 slots.
The starting starship is a C-Class explorer called RF2 Nukyotose with 20 slots and a randomly generated look, equipped with either an Instability Drive, or Sub-Light Amplifier, and a random coloured trail.
The appearance of the player character is completely randomised.