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Auxiliary ships are supply ships that accompany a main fleet, to restock expendable munitions. As specter missiles, grapeshot canisters, rocks and fuel cells are limited in number, it falls to the auxiliary ships to manufacture more of them.

Although most engagements in the Alliance-Syndicate War took place close to supply depots, where fleets could easily be resupplied, some auxiliaries served in the Alliance Navy up to the final battle at Prime. Prior to the First Battle of Prime, at least three fast fleet auxiliary divisions existed, where at least one, the Third Fast Fleet Auxiliaries Division, accompanied the Alliance Fleet to Prime. However, because of their small defensive armament, Syndicate forces inflicted some casualties upon them before the Alliance broke through the Syndic fleet, at least one Titan class auxiliary was destroyed during the fighting, leaving four auxiliary ships to service the fleet. During the lost fleet's run through Syndicate territory, the auxiliaries were critical to it's survival, without them, the fleet would run out of fuel cells before reaching Alliance space. Unfortunately, because of their large mass, the auxiliaries were very slow and difficult to maneuver, even when empty. This commonly makes them the primary target of Syndicate fleets, something that Captain Geary uses to his advantage, drawing enemy forces into attacking the auxiliaries while they are assaulted from multiple angles by the Alliance fleet.

Despite the huge risk the auxiliaries face, only Goblin is lost to enemy forces while close to Alliance space. The remaining three ships make it back to Alliance space, and are reinforced by five extra auxiliary ships, including an extra Titan class ship.

So far, only the Alliance has been seen to use auxiliary ships. Assumingly, because auxiliaries are part of the fleet and the Syndics use private contractors to repair their ships, there are not any in service with Syndicate forces.

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