Due to the high level of training that Solar Federation Engineering teams receive, they are able to replace and upgrade the engines and weapons of a starship very quickly. This can be done at any starbase with adequate components on hand. This process is referred to as the Super Refit mission.
The Super Refit mission is performed in order of ascending starship ID.
When a Super Refit mission is performed, all engines and weapons on the starship are removed. Then, the highest tech complete set of engine, beam and torpedo tube, as appropriate, available will be installed on the starship. It should be noted that if the starship starts with a partial set of beams or torpedo tubes, it could end up with none. Any leftover components will be placed into storage.
The Super Refit mission will also restore lost fighters from starships with the squadron advantage.
Normal starship building takes place before the super refit, so if a starship build uses the parts for the starship performing the Super Refit mission, the refit may not take place, or the starship could receive parts other than those that were intended.
The Super Refit mission takes place before starship movement, so a starship may move the same turn that it is refitted. A starbase will unload any torpedoes that the starship can no longer use, and load any torpedoes of the proper type that are in its inventory onto any starship that refits that turn. Any number of starships may perform the Super Refit mission at a starbase in any given turn.
Example: To perform a Super Refit on a Nova Class you need at least 10 beams of any one type, at least 10 torpedo tubes of any one type, and/or four engines of any one type in storage on the starbase. The engines and weapons on the Nova count towards this requirement.
So let's say your Nova has 10 Plasma Bolts, 8 Mk2s, and Transwarp Engines, and your starbase has 10 Heavy Blasters, 10 X-Ray Lasers, 10 Proton Torpedo Tubes, an even dozen Tech 1 engines, and 5 Mk8 Torpedo Tubes. Your starship selects the Super Refit mission. On the next turn, your starship will have 10 Heavy Blasters and 10 Proton Torpedo Tubes, and it will still have its set of lovely fast Transwarp engines.
See also: Out of Fuel.