When Jaina returns to Hapes, Jag tells her what is been going on since she left.  Jaina wants to talk to the Queen Mother about the incident with Han, but Jag tells her that she may want to wait on that.  After telling Jaina that he doesn't trust Chume, he notices that Tenel Ka overheard the conversation.  Afterwards, Jag and Tenel Ka talk and she tells him that she doesn't particularly trust the former Queen Mother anymore than he does.  She leads him to a darkened empty room where her mother, Teneniel Djo, sits staring out the window.  She talks to the current Queen Mother who does not ever respond to her daughter.  Afterwards, she tells Jag that Chume is not after Leia, she wants Jaina to be Queen.

Harrar and Khalee Lah are able to isolate where they believe Anor's stolen ship has been taken and they summon many ships to help in its return.  The ship is by itself with just one small escort, and that disappoints them as they were hoping for a larger battle.

Jaina and Kyp engage the Vong ships and are able to implant the hybrid seeds into one of them.

As Harrar and Khalee Lah open the captured ship, they quickly realized that it is not the ship they were looking for.  It was a decoy.

After returning from hyperspace, Jaina and Kyp are again followed by a Vong fleet.  Jag and his ships engage the coralskippers as they arrive.  They shoot implants into the coralskippers, and Lowbacca activates a signal that causes the skips to turn around and go the other direction.  With the skips in confusion they began crashing into each other.  Harrar and Lah look on dismayed and make a decision that will probably end Harrar's career - they retreat.

Everyone is thrilled once they land.  Jag says Jaina should consider being a commander with the attack she just pulled off.  After they return Chume reveals her plan to have Jaina take the throne.  Jaina of course thinks the idea is ludicrous.  After unsuccessfully trying to find Jag, she decides to meditate.  She has a vision of having to face her brother Jacen in battle, but this time she kills him.  Kyp awakens her from the trance.  The two of them discuss the lines they are each willing to cross for the greater good.  Jaina realizes she can sense were Jag is and that he may be in some trouble.  She finds it strange, but then realizes that the connection she's grown with him went unnoticed until now.

It seems that Jag was imprisoned for becoming too friendly with the future Hapen Queen.  Jag recounts his troubles and says that it's most likely Teneniel Djo who is the intended target for the former Queen Mother.  They rush to her room but a too late as Tenel Ka kneels by her mother's poisoned body.  Almost immediately the attack alarm goes off.  Tenel Ka rises and then tells Jag that she is placing all of the Navy's fleet under his command.  Jaina realizes that Tenel Ka is actually going to be the next Queen Mother herself.  As they run towards their ships Kyp tells Jag that Jaina would only consider marrying someone who can out fly her.  Jag tells Kyp to take care of Jaina and he agrees.  Kyp runs to try to convince Jaina not to think about sacrificing herself in the Vong ship.  She greets him with a blast of force lightning (which he is able to control) and tricks him off the ship and takes off.

Using the villip Jaina communicates with Tsavong and Khalee Lah and taunts them with the mark of the Trickster goddess she has on her forehead. As the battle begins, Jaina slips deep into the Dark Side and begins taking over total control of the ship.  When the ship is hit by a plasma bolt Jaina feels the pain in her own arms.  She again has the vision of fighting Jacen, but his time she realizes it is Kyp. Jaina realizes all the pain that Kyp has felt from his time spent on the Dark Side.  She realizes it's quite ironic that Kyp is the one to try to bring her back, but that neither of them will know the true nature of the Force for that path is for someone else.  Kyp comes to her aid in battle, but his ship is destroyed.  She picks up Kyp and returns to the surface, leaving Jag and his crew to successfully defend the planet from the Vong attackers.

Former Queen Mother is under arrest for the death of Teneniel Djo.  After leaving a ranting former Queen, Jaina meets with Tenel Ka and the two share a moment before parting ways.  Jaina knows she has a long way back from the person that she's become to what she needs to be.  As Jaina and Kyp fly back to meet Luke, Jaina says that she's probably finished with Rogue Squadron for the time being.  Kyp says he wants to work to establish a new Jedi Council to help bring the Jedi together.  She also agrees to be his apprentice.

Khalee Lah asks Harrar to kill him for his failure.  Lah takes a bomb back to his ship and commits suicide, but Harrar reports that he was killed in battle.  Tsavong Lah wants him to continue the search for Jaina, but Harrah begins to wonder or not Jacen has survived after all.