The Yamashuto-class Colony Ship's engineering room is one of the larger areas of the ship, roughly three decks high, the bay holds the ships main Aetheric Reactor along with four fusion reactors to serve as backup power. It is located below the Yamashuto's computer room. The bay holds most of the ships major electronics, including the main FTL drive and terminals for controlling and monitoring the ships four external engines.

Overhead walkways provide access to more control terminals and also access to maintenance conduits. In the event the ships main bridge is destroyed, or otherwise in capable of functioning, bridge control functionality can be transfered to Engineering.