They have been saving planets and winning wars but still cannot comprehend who is behind the attacks on their ship. First the captain thought that the attacks were jut random and nothing of the sort to be worried about but now he has other views. He thinks that the attacks were always carefully planned and there was a pattern behind all of that. Joshua Dalzelle started adding mystery in the series in The Enemy Within and now the author is just enhancing the impact.
They Omega Force got hold of the ship a long time ago and since then they have taken it as just an ordinary battleship. They are unaware of the secret that are buried within the ship, those who attack on their ship need something that is hidden deep in the ship. The crew even has no clue as what is hidden in the very core of their dear ship. The source of power that the Phoenix possesses is so mighty that the aliens can do anything for its revival.
Now instead of saving the galaxy the Captain and the team has one mission i.e saving their ship so that it might not fall into the wrong hands. New allies are made and the element of sacrifice is surely seen emerging in the troop as we hear a change in the voice of Paul Heitsch in narration. The pitch of the narrator shows that the epic battle is near and for the first time the crew is really concerned about the ending of this whole drama.
The life of the team and the survival of their planet now depend on the security of the source that was always there with them on the ship.