When you’re back in the ship, use the healing point and save your game. Head to the elevator and Emmerson will explain the deal between his faction, the Pangalatic Federation and the other group of highly-advanced humans belonging to the faction called Kronos. When you’re in the Sick Bay, go to where Miki is resting to check up on her. This will start a lenghty cutscene with Fidel, Fiore, and Miki being beamed down back to Faykreed IV. The cutscene will continue with the Charles D. Goale and the allied Federation ships, Akagi and Nimitz being attacked by a fleet of Kronos vessels.
After suffering considerable damage and defeat against the Kronos fleet and making some arrangements with the Kronos captain, Emmerson devises a plan to save the crew of the other ships and keep Relia safe from the enemy.
Once you’re in control, you’ll be controlling Relia. After some conversation with Anne and Emmerson, head to the transporter to continue with the cutscenes.