A ship captained by a man named Roy Scantron arrives at Prion Control Galactic Transport Hub.

Jax looks at old pictures of her and Greg. Zazie comes in and wonders about their study group with Ralen and Jett both off-planet.

While discussing Greg, Jax suddenly gets ill, seeing double and flushing a strange color.

On Prion Control, Scantron wants to take the Earth Com cargo but he's not insured properly. The comptroller gives him some Parallax containers to deliver, warning him not to look inside ever. Scantron questions whether it's illegal but when the comptroller tells him how much the job pays, he agrees to the job.

Once the comptroller reports that Scantron's taken the job, his contact sends killers in to take care of him.

Jax returns to her room and tells Zazie that she's pregnant.

Sector 5378, Non-aligned Territories. Jett, Xander, and Ralen are following Scantron's transport, tracking the signal of Parallax munitions they took off the Sumi pirates. They monitor the ship's coms and hears the captain singing.

Jax tries to contact Xander about the pregnancy. She confides in Zazie that she wants to terminate the pregnancy. Zazie tries to convince her she'd be a good mother. Suddenly, Jax has a substantial baby bump and the baby's moving.

Jett, Xander, and Ralen board Scantron's ship and arrest him for transporting illegal weapons. He claims ignorance about his cargo.

Jett opens up the containers and they find people inside, held in stasis.

Jett discovers that all the people are clones manufactured on Adar from the cells of dead Earth Com soldiers. As Jett scrolls through the identities of the clones' original people, Xander sees his own brother, Zion, among them.

Finding Zion, Xander asks Jett to wake him. Ralen argues that the clone is not his brother but Xander insists. When he revives, Zion asks for the Commander, not seeming to recognize Xander at all.

Jax discusses her pregnancy with Schral who informs her the child is not Xander's. She is pregnant with her own clone. She wants Shral and Osborn to find the baby new parents.

She goes into labor while in his office.

Xander talks to the Zion clone, trying to revive memories.

Jax and Zazie brings the baby into the school cafeteria. Jax is bonding with her.

Xander shares his relationship with Zion with Ralen who warns him about living in the past. Their ship is flanked by multiple enemy ships.

Jax names the baby Bloom.

Xander identifies the enemy ships as Bellum Batonianum, violent secessionists who want the Outer Rim colonies to break away from the Earth Confederacy.

Scantron shares that his ship has no weapons or shields. He starts to panic and Xander sens him off the bridge. He runs off.

Ralen suggests hiding some mines in trash containers and dropping them behind the ship. The ruse takes out one ship but there are still four more. The ship suddenly loses all power.

Scantron sneaks onto the Earth Com shuttle and leaves the ship. The Bellum Batonianum board the ship. They are led by the Courier from the season premiere, introducing himself as Bay Turan.

Turan is able to command Zion and orders him to bring him to the others. Once the other clones are taken, Turan orders Zion to stay and asks Xander why he is special. He threatens to kill Zion.

Shral checks in on Bloom and Jax. Jax is protective and refuses to let Shral examine the baby. She asks for one more night with Bloom before giving her up.

Xander admits he woke Zion because he is the clone of his brother. Turan orders Zion to kill Xander.

Zion hesitates and Turan orders his men to kill them all. Zion's memories are restored. A firefight ensues and Zion is hit. Turan orders his men to grab the clone and head back to the ship. Ralen holds back Xander and tells him they'll find Zion since he's placed a tracker on him.

Turan's ships fire a torpedo at the ship but it is neutralized by a shot from Scantron in the stolen shuttle. He's brought the Dauntless back with him and they pursue the marauders as they flee.

Jax prepares to be a mother to Bloom, promising she'll never let anything happen to her. She goes to sleep but Zazie's only faking sleep across the room.

Scantron shares that he plans to reconnect with his sister, Bertha.

Jett gathers some information and discovers that the clones were created by TN5, Parallax's competitor.

Jax wakes up and discovers Bloom is gone and so is Zazie.