How do I repair the capital ship?

[garm]

2 ways to repair a ship:
- equip a repair system which you can sometimes buy at a trading station
- leave the system through a portal

They both work for capital and fighter ships.

[Kzak]

Repair systems for the mothership are worth their weight in gold for those tough missions. But as the above poster states, the mothership will be fully repaired if you move to another star system.