Small craft make a single threshold check after losing half of their hull boxes. Roll 1d6 for each system, on a roll of 4 or higher the system is completely destroyed (even for beam and jump drive systems). In addition to the systems listed below, all small craft have a single drive system which, if damaged, prevents them from moving for the duration of the engagement. Small craft are moved and conduct attacks as fighters. Small craft may be targeted by capital ships with any weapon capable of engaging a fighter, fighters however, target them as capital ships. Though often armed with Pulse-1 batteries, they are limited to a 6 MU maximum range. They attack fighters using the optional rules for engaging fighters with pulse-1 batteries (no effect on a roll of 1-3, one fighter hit on a roll of 4-5, and two fighters hit on a 6, with an additional reroll). Small craft armed with beam weapons may only engage targets within 6 MU, and destroy 1d6-2 fighters. They may not screen, but do not have to engage screening fighters when attacking a capital ship. Individual small craft are launched and recovered as a fighter squadron.

A capital ship can typically carry 2 shuttles for each fighter squadron it can carry (though generally only carry half this number, the extra space reserved for visitors). These shuttles can be carried simultaneously with the fighters. Fighter squadrons may be replaced with shuttles for additional transport, with 2 shuttles replacing each fighter squadron. A Nova for example, could carry up to 16 shuttles if it replaced all of its fighters with shuttles. Vessels without fighter bays are typicaly able to carry one or two shuttles.