The Mothership Fleet refers to the fleet used to escort the Hiigaran mothership be it the original Kushan Mothership or the later Pride of Hiigara. It is unclear whether or not the Mothership Fleet is actually an institutionalized fleet to which people are recruited or whether it just happens to be whatever fleet is traveling with a Kushan mothership.
The First Mothership Fleet
During the Exodus, the Kushan constructed a small and mostly ceremonial escort for the Mothership should she come into danger's way. This was composed of seven small Scout and one Resource Collector. Gradually, Interceptors, Light Corvettes, Heavy Corvettes were added to the fleet. Even so, it was hardly a fleet with which to contend with in a galactic war.
Upon learning of the Kharakian Genocide however the Kushan leapt into action, recruiting as many pilots and crew members for war as they could, even waking frozen men and women from the rescued Cryo Trays. By the time the Kushan had reached the Great Wastelands they had begun construction on several frigate-sized vessels and had vastly expanded their strike craft forces.
The Mothership Fleet also expanded by acquiring new ships through capture. Rather than bother to construct new vessels every time they needed one the Kushan utilized the Salvage Corvette to pirate ships from their enemies. This allowed the Kushan fleet to expand rapidly.
Constantly the Mothership Fleet was updating itself with new technology. Many of this early technology was based on pirated vessels or scans of enemy ships. This led to the advent of such technology as Plasma Bomb, cloaking devices, and proximity sensors. Other technology was bought from the Bentusi. The most important of these purchases was ion cannon technology which allowed the Kushan to fight on par with the Empire. Other technologies were developed by the Kushan independent of outside forces. All of the chassis and drives used by the Mothership Fleet were independently designed and the Kushan also developed fast-tracking turrets on their own in order to fight off the Kadeshi.
By the time the Mothership Fleet reached Hiigara it had reached considerable size and was able with the help of the Taiidan Rebels to defeat the Taiidan Elite Guard and destroy the Emperor's flagship.
It is likely that in the years following the Homeworld War the Mothership Fleet was kept intact and active in order to protect the Hiigara system from invaders. The Mothership itself however was retired and used as a new shipyard for constructing more fleets for the Hiigaran government. In the meantime, the Mothership Fleet along with the Galactic Council would provide for the security of the Hiigaran state. Eventually this fleet too would be retired, replaced instead by kiith-based fleets.
The colors of the first Mothership Fleet were gray and white.
The Second Mothership Fleet
Prior to the Vaygr War the Kushan again began to construct a new mothership called the Pride of Hiigara. Meant to be the flagship of a new defense fleet which would mobilize against the growing Vaygr threat its launch procedures were interrupted by a Vaygr surprise attack. Retreating the Pride of Hiigara, like the first mothership, was forced to build up an escort fleet nearly from scratch.
It had more people with whom to do so however. Hiigaran transports arrived with thousands of crew members willing to serve in the new Mothership Fleet, all of whom were quickly given positions in the Fleet, which then departed from a besieged Hiigara.
The new Mothership Fleet grew quickly and by the Battle of Gehenna had reached considerable size. This was to be expected however as the Kushan had already developed the technology necessary to run their fleet. The most important advance in the second Mothership Fleet therefore was the addition of Progenitor technology.
During the quest for the Sajuuk the Kushan recovered several artifacts of Progenitor technology which helped them develop weapons more effective than those used by the Vaygr. This included mover technology, which allowed the Kushan to build highly advanced AI construction and maintenance vessels capable of taking on frigates in small numbers. Another powerful addition was the recovery of the Gatekeeper of Sajuuk, a powerful Progenitor Dreadnaught armed with a Phased Cannon Array. This ship alone helped the Kushan win new victories.
Near the end of the Vaygr War the role of the Mothership Fleet changed. The Pride of Hiigara was abandoned upon the discovery and recovery of the Sajuuk, left behind in the wastes of Balcora. The Mothership Fleet's new goal was to escort the Sajuuk, a job to which the Fleet took well. Relieving the other Hiigaran defense forces at the Siege of Hiigara, the Mothership Fleet and its flagship became instrumental in repelling the Vaygr invasion once and for all.
The colors of the second Mothership Fleet were light blue and white.