Aboard an EarthForce explorer vessel, Lt. John Matheson breaks up a fight between the Martian crewmen and their Earth counterparts. The crew has received word that the ship has been ordered back to the plague-infested Earth after the Drakh attack, and the Martian crewmen have no interest in risking their lives for the planet. Ensign James speaks for the Martians, asking who is with him. James and a few of his men fight their way past security, only to come face-to-face with Captain Matthew Gideon. Gideon tells James that he's welcome to try taking over the ship... if he can beat Gideon. James accepts the challenge but Gideon easily beats him and orders the other Martian crewmen to back off. As Matheson arrives, Gideon reminds the crew that he kept them alive through their mission and he has no plans on letting them die. They calm down and Gideon tells them that he'll forget what happened.
Matheson confirms that no one was hurt as Gideon receives word that they've arrived at Earth. The two officers go to the viewing port and see the ruins of dozens of EarthForce ships in orbit, destroyed trying to repel the Drakh attack.
Later, Gideon is in his quarters watching an ISN report on the death toll when Matheson comes in. The captain tells him what little they've found out about the Drakh and regrets not being there to help the fleet. Matheson points out that even if they had known in time and had a destroyer rather than an exploratory vessel, they couldn't have gotten there in time to make a difference. The first officer says that James is recovering in sickbay and the doctor recommends that Gideon press charges. James' father is a highly-placed officer on Mars and Matheson warns that the man could make trouble for Gideon when word gets out that the captain struck a crewman. Gideon thinks that they have bigger issues to worry about and isn't concerned... until they get new orders that Gideon should go immediately to Mars.
As the exploratory ship jumps into hyperspace, the technomage Galen monitors it and says that "it" is beginning.
Several sectors away, Captain Henson and his crew open fire on a Drakh ship near Ceti 4. The Drakh vessel is one of the ones that unleashed the plague on Earth, and is returning fire. Henson manages to disable the Drakh ship and send a message to EarthForce just as a shot hits Henson's vessel, blowing up the reactor and the ship.
On the planet's surface, archaeologist Max Eilerson with the IPX is working at an alien ruin. He sees a flaming object descend through the planet's atmosphere and calls in to his underling, Sam. Eilerson has her send Jenson in one of their two shuttles to see what it is. The debris landed near a rumored underground city that the IPX archaeological team will be investigating in a few days.
The Drakh ship crashes to earth and the crewmen start to emerge.
When they arrive at Mars, Gideon meets with Senator McQuate and the Martian military liaison, Mr. Ames. When the captain comes in, Ames is arguing with McQuate, claiming that Gideon isn't right for the job. Gideon assumes that he's there about the mutiny and starts to explain, but McQuate cuts him off and brings up footage of the riots on Earth. Scientists have worked out that it will take five years for the Drakh plague to adapt to humans... and wipe out every last one on Earth. McQuate points out that Mars is a dead world and that Earth could be the same, and Ames notes that there is almost no chance of someone finding a cure in five years. EarthForce is sending out as many ships as they can to find a cure, or other traces of the plague, or an alien race with sufficient technology to develop a cure. The government is spearheading the effort with a prototype destroyer, Excalibur... and they want Gideon in command. When Gideon wonders why they chose him, McQuate explains that he has a reputation as a dangerous man, and he's encountered more alien life forms than any other EarthForce commander. Gideon accepts but Ames warns him that it is a prestige mission and the government will choose some of the crew. Undeterred, Gideon accepts but warns them that he's not subtle... but he'll get the job done.
On Ceti 4, Jenson flies over the Drakh ship and reports in that the wreckage is a ship. Drakh crewmen open fire on him, blowing up the shuttle.
At the IPX outpost, Eilerson and Sam listen to Jenson's last message. Sam warns that the planet's atmosphere is too heavily ionized to let them get a message through to the parent company, and the next transport won't return for two weeks. The mission team's pilot, Trace Miller, suggests that they evacuate immediately, figuring out the aliens are hostile. He notes that they made no attempt to contact them and opened fire immediately. Since they only have one shuttle left, Trace proposes that everyone move into the caves near the rumored city while he takes the shuttle up and sends a SOS. Eilerson warns that the unknown aliens will undoubtedly have sent a SOS of their own, but Trace says that he has no plan on dying.
On Mars, McQuate introduces Gideon to the scientists chosen for the mission. They are still short an archaeologist and a linguist. Dr. Sarah Chambers comes in last and McQuate explains that she'll be serving as chief medical officer and Gideon's liaison with the scientists. Chambers is unhappy that no one has said why she's there and demands to return to Earth despite the plague. Her sister Jenny is there and Chambers believes that she could do more good planetside. McQuate tells her that they have an important job for her and the others. However, before he can explain, an aide comes in and says that the prisoner has gotten away.
While McQuate goes to check out the prisoner, Chambers asks Gideon for an explanation. He starts to tell her just as a security team drags in the missing prisoner: Dureena Nafeel. A thief, she has escaped detention and insists that she's supposed to be aboard Excalibur. McQuate orders his guards to lock her up, but Gideon insists on talking with her. As they leave, Gideon tells McQuate that he wants Matheson as his first officer. McQuate reminds Gideon that Matheson is a telepath and that there is still heavy prejudice against them due to the abuses of Psi Corps. Undeterred, Gideon says that Matheson has followed all regulations concerning telepaths and that he'll have his friend with him.
In the cells, Dureen explains that the Drakh killed her people, and she's been following them ever since to keep them from doing the same to other planets. McQuate explains that Dureena is a member of the thieves' guild and they've been holding her in protective custody so that she can give them information on the guild. The senator is also concerned about the image having a thief on the team will mean for such a prestigious mission. Dureen tells Gideon that she's an expert thief and that they will need one where they're going. Gideon agrees, telling McQuate that he's taking Dureena with him.
The crew takes shuttles up to Excalibur and admires the huge prototype destroyer. Matheson greets them and thanks Gideon for standing up for him. He then tells the captain that he's set coordinates for the testing area in an unoccupied sector of space. Chambers goes to check on the medical labs and Dureena tells the two officers that one more crewman will be joining them. However, she refuses to say who it is, and claims that he can come and go when he wishes. Once she leaves, Matheson worries that his being a telepath may have caused trouble. Gideon assures him that he insisted on having the best man for the job.
As Excalibur jumps into hyperspace, Galen continues following them.
Once Trace takes the shuttle into space, he tries to send the distress signal but discovers that he doesn't have enough power. The ship's computer detects an EarthForce military distress beacon and Trace sets course for it in the hopes he can piggyback his signal on the beacon's.
As Excalibur heads for the testing ground, McQuate calls Gideon on a private channel and tells him that he's to head immediately to Ceti 4. The destroyer is the closest ship to the planet and McQuate informs Gideon that there's a team of civilian archaeologists there. Once McQuate signs off, Gideon starts to leave but a voice speaks from the shadows, a voice without a source. The voice addresses Gideon by name, and says that he'll be there when the captain needs help. Gideon doesn't recognize the speaker--Galen--who tells him to expect him when he sees him.
Once they arrive in orbit above Ceti 4, Gideon takes down a flight of Starfuries and a shuttle with Dureena and Chamber. While Chambers prepares to scan for contamination aboard the wreckage, Matheson calls to report that they've received no response to hails. Gideon tells his first office to check the comm system and find out where the message from Galen came from.
On Ceti 4, Trace and the others go to the caves where they've found the legendary underground city. The pilot spots the Drakh soldiers approaching their position and goes inside to warn Eilerson. Gideon contacts them by radio and tells them to keep the signal going so that they can home in on their position. Eilerson tells Gideon that the Drakh are closing in and the captain sends some of the fighters to wipe them out.
At the Drakh ship, Counselor L'shan and his remaining soldiers get word that that their soldiers have been wiped out. L'shan contacts the Drakh fleet captain, who tells him that reinforcements are on the way.
Gideon and the team land at the city and start evacuating the archaeologists. The captain asks Eilerson to take them to the crashed Drakh ship, and Trace is eager to help. Eilerson isn't, figuring that Drakh reinforcements are on their way. When Gideon wonders how he knows, Eilerson explains that he managed to decrypt the Drakh ship's distress message and translate it. Impressed at his skills, Gideon tells Eilerson that he'll go with them or they'll leave him behind, and the archaeologist soon gives in.
Eilerson takes Gideon and his team to the Drakh ship and they board it, wearing rebreathers to protect against the plague if it was released in the crash. Chambers confirms that there is no trace of the plague in the atmosphere just as Drakh soldiers open fire on them. Dureena circles around behind them and plants an explosive charge, killing them.
The Drakh fleet comes out of hyperspace above Ceti 4 and Matheson warns Gideon that they have a fight on their hands. Gideon orders the Starfuries into position and Trace volunteers to take the captain back to Excalibur to coordinate the defense. They leave after Gideon tells the team to stay behind and find the commanding officer that the Drakh soldiers were protecting. As Gideon leaves, a Drakh soldier prepares to ambush him... and Galen arrives and kills it. He tells Gideon that he'll be there when Gideon needs him and then disappears.
In the Drakh wreck's central chamber, fog suddenly pours in. Dureen realizes that Galen has arrived and they start searching for the ship's captain. A Drakh soldier tries to ambush them and Galen kills him.
Trace gets Gideon back to Excalibur and the captain coordinates the attack on the Drakh fleet.
Aboard the Drakh wreck, Dureena and the others find L'shan. Dureena looks behind them and sees Galen, her ally from the Drakh attack on Earth. Satisfied, Galen walks away.
Excalibur wipes out all of the Drakh ships except one, and it tries to ram them. Gideon has Matheson fire the ship's main weapon, despite the fact it will leave them with minimum power for one minute. The risk pays off and the ground team calls to report that they've captured L'shan. Satisfied, Gideon has Matheson send a shuttle for the ground team.
Later, Eilerson acts as translator as Gideon interrogates L'shan. The Drakh refuses to betray his people and refuses to answer any questions. Gideon figures that they can work out a cure to the plague from the samples aboard L'shan's ship, and informs the counselor that he'll be sent back to Earth and exposed to the plague. When the Drakh reveals that he understands what Gideon is saying without translation, he asks Gideon who he serves and who he will be when Earth's population dies from the plague.
As Gideon leaves the interrogation room, Matheson reports in with him. The captain tells him to sign on Trace and Eilerson, despite Eilerson's attitude. Before he goes, Matheson gives Gideon the coordinates of Galen's message and Gideon remembers what happened the last time he was there nine years ago.
After his ship is destroyed, Gideon floats in space, his oxygen running out. He sees a fleet of technomage ships pass by him and desperately calls out to help. One of them finally turns and comes back for him.
Gideon tells Matheson to take Excalibur to the coordinates.
In her quarters, Chambers tapes a message for her sister Jenny. She says that that she doesn't know when she'll be back but promises to find a cure for the plague.
When Excalibur reaches Galen's coordinates, Gideon goes down to the planet and finds Galen waiting for him. The captain finally recognizes him as the technomage that saved his life nine years ago, and wonders why he is there. Galen explains that the technomages banished him from their circle because he chose to help humanity and had too much contact with them. His people believed that he risked exposing their hidden location and exiled him. Since then, Galen has been watching Gideon to determine if he should help him and risk further punishment. The technomage says that he can help if Gideon asks, and the captain asks. Galen responds by asking him who he is, who does he serve, and who does he trust. Gideon admits that he doesn't know the answer to the last two questions, and at that Galen says that he'll go with him.