See this for the back story- http://scifi.wikia.com/wiki/Talk:The_Collaborative_Writing_Project:_The_Great_Starship_Battle#Quick_note_for_anyone_interested_in_continuing_this_story!
Wedge Antilles enters the story line as he flys from the surface of the distant forest moon of Cleavack wondering what the hell was going on. The com's traffic was heavy and it seamed like a war had broken out.
Spock stayed behind, with Yoda and Jarjar Binks in Spock's Jellyfish ship. Wedge finds the empty and moderately damaged Battelstar Battlestar Athena, boards it and finds it empty and abandoned except for a few DEAD replicators and a few DEAD crewmen.
A lightly damaged Slave 1 was abandoned and floating about by it. In the far distance he can see a damaged Battlestar Atlantia adrift and abandoned like the Athena.
A few small peaces of debris from the USS Enterprise's inner hull also drift past. He stabilizes the Athena's position in geo-sycrinose orbit with the planet, with Slave 1 left in suite, and returns to Spock, Yoda and Jarjar Binks. Skagra's Invisible Spaceship was parked next to Spock's Jellyfish.
What happens next is up to others to write.