The episode opens with a recap of what happened in part 1 - namely the reawakening of Epsilon 3 and a large ship coming through the jump gate. The ship turns out to be Starship Hyperion, a heavy cruiser sent by Earth to take control of the situation and ownership of the technology on the planet below. Since Babylon 5 is neutral territory, Earth feels that all of the other races will want a part of what was found. Captain Pierce is there to make sure it doesn't happen with a show of force.
Sinclair's authority being questioned or usurped is a recurring theme in the show, happening at least four times already in this season with the most recent example being Eyes only three episodes before (two if you count the two-parter as a single episode). As usual, he pushes back. He speaks to Senator Hidoshi to demand clarification of the situation - he was promised he had the final authority over the sector, and threatens to resign in protest. Given the number of people trying to wrest control from him, and the awkward political situations he's caused, this doesn't seem like the best plan.
Pierce sends fighters down from the Hyperion, which are stopped by the planet's defence systems which are escalating in response to the threat. Sinclair buys time by telling Pierce that his own shuttle only got to the surface by using a jamming device. It delays Pierce, but now they have a bigger problem: the approach of the fighters triggered further earthquakes. In 48 hours they'll cause the planet's advanced fusion reactors to blow and the explosion will take Babylon 5 with it. Evacuating the station will take at least five days.
Pierce, being a typical Earthforce knucklehead, decides to send further fighters down. Sinclair responds by announcing a planetary blockade - any ships trying to land will be shot down by Babylon 5's own fighters. It solves the immediate problem, but then a strange ship comes through the jump gate. The captain announces himself as Takarn, whose people have been searching for the planet for 500 years and claim it belongs to them. All others must move aside within ten hours or be destroyed.
Pierce's response is to give Takarn nine hours to withdraw.
Things are just as explosive on Mars. President Santiago has sent shock troops to subdue the rebellion. Watching the news in a bar, Garibaldi overhears a customer calling for Mars to be nuked and assaults him. Sinclair later finds him to give a gentle reprimand, and Garibaldi admits that uncertainty over the fate of old girlfriend Lise caused him to snap. Sinclair makes him a deal: he'll call in some favours to get Garibaldi a clear channel to Mars, if Garibaldi promises to make sure that if the station is evacuated Ivanova is on the last ship out.
Draal hears Varn, the Epsilon 3 alien, calling to him just as Sinclair and Londo did before. He visits medlab where the ever skeptical Doctor Franklin tells him the patient is comatose and couldn't possibly have been sending him messages. However Varn wakes and confirms what Sinclair has already guessed - the defences on Epsilon 3 are escalating because the machine no longer has a "heart".
Varn reveals Takarn's people were cast out centuries ago by the race that built the machines. He has been one with the machine for 500 years, but now he's dying. Sinclair, Draal, and Londo all saw him call to them. He can't ask directly, but one of them must replace him. Delenn wonders why he chose these three, and Draal suggests that is was "Perhaps because we are familiar with the third principle of sentient life", the capacity for self-sacrifice. Draal and Sinclair seem obvious choices, Londo less so. It's only later we'll see the lengths he'll go to for his people, and perhaps that the machine chooses him now is an indication that - despite what's to come - he's not yet at the point where he'll make terrible choices.
Delenn, Draal, and Londo take Varn back to the planet, leaving Sinclair behind. Their shuttle sparks a battle, with Takarn firing on the Hyperion and Babylon 5 wading in to support the Earth Force ship. Garibaldi grabs another shuttle and goes after them thinking Varn has been kidnapped. What he finds when he gets there is Draal preparing to go into the machine. Draal plugs in and announces to the warring factions that the machine belongs to none of them. He trusts the Babylon 5 Advisory Council to ensure Epsilon 3 is left alone until the time is right, but that if this can't be managed the planet will defend itself against all comers. Of course Takarn doesn't listen and is destroyed.
It's a definite deus-ex-machina ending, but one that's earned by what goes before.
Varn assures Delenn that he'll spend his remaining days watching over Draal, who will see wonders in the heart of the machine - "He will see all the tomorrows. Hear all the songs. Touch the edge of the universe with his thoughts". Sad to lose a friend, but glad he's found a purpose, Delenn quotes the third principle of sentient life back to Draal and says goodbye.
With Epsilon 3 now off limits, the Hyperion leaves and Pierce apologises to Sinclair for overstepping. Sinclair goes to tell Garibaldi contact has been made with Lise. She informs Garibaldi she's married now, and expecting a child. It seems like a damp squib of a plotline, except that Lise will be important later.
Most of the ways the episode ties into the wider plot aren't obvious - both Lise and Epsilon 3 are guns being put into drawers for later. However the episode doesn't feel completely disconnected as it links back to the mystery surrounding Sinclair. Garibaldi asks Delenn why they took Varn in secret, without telling the commander. She replies that if she had Sinclair would now be in the machine, but his destiny lies elsewhere. She also now owes Londo a favour for piloting the shuttle to the surface, and is sure he will collect. He does, but not until season three. While it's not an obvious lynchpin at first, viewed in hindsight this episode is essential in building future arcs.