don't worry you didn't miss much, all you do is fly back to the carrier, get checked out, Prophet goes nuts and flies back to the island, the navy nukes the island which gives the aliens the energy source they were looking for. The aliens attack the carrier, you get in a big battle, have to shut down a nuclear reactor, get back to the flight deck, take out the big spider looking alien monster and then take out an alien warship or something with your tac gun
then the game is over, the australian dude and the asian chick save you and you fly back to the island because prophet contacts you as the carrier and the alien warship sink into the ocean. The end