Imperial Command Ships
Ships of Leaders for the Imperial Navy
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Aquila Class Imperial Command Ship

Name: Aquila Crysaetos

The Aquila Command ships were designed for delivery to high ranking Imperial officials. While under construction a planned sneak attack on the manufacturing and research facility caused much panic. The temporary captains fled with their under-crewed and under construction ships into the systems nearby dense asteroid field in a hope to hide them.  While they fled the research base was inevitably ransacked. If the ships could not successfully flee all the proof of existence of the command ships would be destroyed or captured by the Chaos attackers.
None of them were able to make contact with any other Imperial forces and all was thought to be lost. Only recently one command ship was found by a cobra squadron on a patrol mission in the system. The ship was discovered intact from the unique radiation emitted in the field that kept  it hidden from sensors. With this discovery the cobra crews found out from the captains logs, that there were at least two more of these command ships in existence and in a desperate attempt to stay concealed the void shield were not raised and the deadly radiation soon overcame the crew.
Finished and repaired, the single found Aquila ship named Aquila Chrysaetos was entered into service. Too late to be delivered directly to the Emperor, but a test run of service would determine if it was ready for use for other high ranking officials. 
The System was blockaded and Imperial forces continue to search for the other two known aquilas.
Super Emperor Class Imperial Command Ship

Name: Claimh Solais

Command ships are rarely seen in any battles except full scale fleet engagements. The super emperor does not only act as a heavy gunship, but as a full fleet carrier, able to help out in the most dire circumstances. If it is not out patrolling the voids of space it is seen orbiting high priority planets or military installations.