Use the transporters to beam fuel and cargo onto and off the ship. New ships begin the game with no fuel, unless the starbase primary mission is set to refuel.
Player one (The Solar Federation) is the only race that can upgrade the tech levels of an old starship. Their ships can set their mission to "Super Refit".
The Starbase can also recycle old ships. When a ship is recycled, using the recycle command, all the ship's beam weapons and engines are removed and placed into storage. The hull is converted into minerals and stored on the planets surface. The ships torpedo tubes and torpedoes are also removed and placed in storage.