The ship coming through the jump gate is an Earthforce Hyperion-Class Heavy Cruiser. Captain Ellis Pierce (Ron Canada) announces that he is assuming control of Babylon Five. The alien brought back from Epsilon III is in Medlab. Doctor Franklin (Richard Biggs) was able to stabilize him, but he remains unconscious. Commander Sinclair (Michael O’Hare) meets with Captain Pierce in his office. Pierce explains that the Office of Planetary Security wants to make sure that no-one except Earth Alliance could claim the revolutionary technology found on the planet below. Sinclair is less than pleased and thinks Pierce’s show of force will stir up unnecessary trouble.

The ISN broadcasts that President Santiago is increasing the forces sent to quell the rioting on Mars. Michael Garibaldi (Jerry Doyle) listens in a bar, despondent, drinking water, with no news of his ex-girlfriend on that planet. When someone suggests a nuclear solution to the rioting, Garibaldi corrects him in a physical way. Sinclair contacts Senator Hidoshi (Aki Aleong) about Captain Pierce and will not share authority without a direct order from the President. He threatens to resign, and the Senator promises to do what he can. Ivanova calls him to C & C and explains that a Starfury wing from the Hyperion is heading for Epsilon III. The planet’s automated defense system may prevent them from getting through and Sinclair says so to the Captain. Ivanova points out the disruptions in the planet’s core, which could destroy the planet, along with Babylon Five and the Hyperion.

At a meeting with Sinclair, Garibaldi, and Ivanova, it is determined that the planet contains a series of enormous fusion reactors nearing a critical state. It will take three to five days to evacuate the station. They believe the alien was keeping it all in check. Ambassador Mollari (Peter Jurasik) wants to be in the loop, but Ivanova brushes him off. Delenn (Mira Furlan) and Draal (Louis Turenne) investigate a voice calling Draal. Sinclair calls on the distraught Garibaldi and promises to get him information, then asks him to make sure Ivanova escapes if it all goes sideways.

Delenn and Draal find the alien Varn (Curt Lowens) in Medlab, who has been calling to Draal. Doctor Franklin points out that Varn is unconscious, just as Varn awakens and warns them that the planet will explode if approached unless it is with “another”. Nevertheless, the Hyperion is preparing to send down more Starfuries. Sinclair threatens to attack the Hyperion ship, since they will all be destroyed anyway. Suddenly, another colossal enemy ship comes through the gate and fires a beam at the Hyperion and the station.

The beam is a communications scan. The ship’s captain, Takarn (Michelan Sisti) is of Varn’s race. He says his people have been searching for the machine on Epsilon III for 500 years. They will take the planet by force if necessary, in ten hours. Pierce orders them to withdraw in nine. Sinclair speaks to Varn, who says the Great Machine on the planet was purposely hidden there, and he has been living in the heart of the machine for 500 years to keep it away from these very people. Babylon Five belongs to the future, and the outcasts must not have it. Then he passes out again. The Doctor says he has begun to die and that is why the machine has been malfunctioning.

Delenn and Draal admit that they both know what Varn means by “another”. Mollari shows up to speak to them. Pierce contacts Sinclair. Takarn’s ship is jamming both the station and the Hyperion, and they reluctantly agree to attack the alien ship together. Londo tells Delenn and Draal that Varn appeared to him as well and agrees to help them. Ivanova authorizes a Centauri launch and Garibaldi reports that someone has taken Varn from Medlab. The Centauri ship heads for the planet with Mollari at the controls. Delenn, Draal, and Varn are aboard. Takarn’s ship opens fire on everybody at once and the Battle of Epsilon III has begun.

The planet’s defense systems do not fire on the Centauri shuttle. Garibaldi goes after them in his own shuttle. He arrives to find Varn about to hand the machine over to Draal. The battle above begins to go badly, but Draal appears to the three commanders, telling them the planet belongs to none of them. He entrusts the region to the Babylon Five Advisory Council if they will maintain the planetary quarantine. The planet’s defenses are now operational. Takarn’s ship starts to approach and is destroyed. Draal’s thoughts will now reach across the universe. Delenn says her farewell.

The Hyperion is leaving. Lise Hampton (Denise Gentile), on Mars, is injured but alive and wants to speak to Garibaldi. She’s married, actually, and pregnant. Michael, crushed, congratulates her. Later, Delenn approaches him on the observation deck. She tells him that she did not take others into her confidence because Sinclair would have taken over as the new Guardian as he is a True Seeker, and his destiny lies elsewhere.

In later episodes, Straczynski played down the giant machine under Draal’s control, lest a Deus ex Machina eclipse the problem-solving of people, which is key to the series. One of the Hyperion’s fighters is numbered THX-1138, George Lucas’ license number as a kid and the title of his first movie. The Hyperion was a rare survivor of the Battle of the Line in the Minbari War. New ships will appear later. Among the terms downloaded by the aliens’ communications scan are the word Skynet from Terminator and the phrase I am Not a Number from the Prisoner. Fusion reactors do not explode. Captain Pierce has seniority by right of rank, Sinclair by right of position. Pierce is not in Sinclair’s chain of command and has no power over him. Aside from the great ships and the battles, perhaps the best part of the story is Londo Mollari saving the day as a shuttle-pilot and Ivanova’s summation of the conflict: “Worst case of testosterone-poisoning I’ve ever seen.”