This is a bit of an odd episode because most of what it does is set up for the things that will happen in part 2 and beyond, and move on pieces of plot that have been set up earlier in the series.
The main plot is that seismic disturbances on Epsilon 3 suggest it isn't as dead as everyone thought. There appears to be some sort of automated defence system deep within the planet that was triggered by the quake, which disables the ship of the science team sent down to investigate. Although Babylon 5 orbits it so far Epsilon 3's been little more than space furniture, so everyone's excited about the prospect of exploring an potentially inhabited world. Shortly after Sinclair sees an alien begging for help, which disappears before his eyes. Londo later sees the same figure, although he's drunk at the time.
Sinclair and Ivanova go down in a shuttle after fooling the defense system to target the fighter's they've brought along as a decoy. Once past the missiles they find a clearly artificial opening, which leads to a landing pad and an advanced installation with "machines as big as buildings". The alien appears again, this time to both of them, and warns that if they don't help a lot of people will die. They find him plugged into the machine at the centre, and extract him to take back to Babylon 5.
Back on the station Delenn is visited by Draal, an old friend and teacher, who teases her to answer what is the third principle of sentient life (the answer being "the capacity for self-sacrifice. The ability to override evolution and self-preservation for a cause, a friend, a loved one"). I love how this relationship is depicted, as one of mutual respect and warmth, in the same was as her friendship with Shaal Maya in "The War Prayer". They tease each other, but in a very Minbari way. And now that I think about it, I don't remember that we ever see any of the other ambassadors having this kind of relationship with another of their people.
It turns out Draal has come to say goodbye. Minbar has changed too much, and he sees discontent everywhere (see above quotation). He tells Delenn he's going "to the sea", which at first sounds like a euphemism for some sort of Dignitas arrangement, until he tells her it's because he wants to find somewhere to be of service before the end. It's not made clear what this means exactly, except that Delenn will never see him again.
The discontent that Draal sees on Minbar is mirrored in the news of what's happening on Mars. The agitation mentioned in previous episodes has blown up into full rebellion against the Earth government. Mars has been cut off - no communication can get in or out amid reports of fighting in the streets and casualties in the hundreds. Garibaldi's trying to get through the blackout to find out the fate of ex-girlfriend Lise Hampton, with whom he parted on bad terms over going to Babylon 5. Even his high level clearances aren't enough to get through, so in desperation he turns to Talia Winters to use her connections in Psi Corps. Talia's less than pleased to see him, since he's apparently been stalking her. It's played for laughs, which is frankly creepy, although it may be an in joke as the actors were married at the time. Talia isn't able to get him access to Psi Corps' communications, but she does find out that Lise isn't listed among the known survivors.
There are also a couple of appearances from Ambassador Mollari in the episode, as usual doing double duty as both a comic and tragic figure. When Delenn takes Draal to meet him, he's busy trying to decode one of the many variations of the Hokey Cokey. Earlier in the episode he has a diplomatic meeting with Sinclair and Delenn to negotiate a trade agreement. He mentions how much easier these meetings are without Ambassador G'Kar present, and the topic of the hatred the Narn and Centauri hold for each other comes up. "they will do anything to destroy us until the universe itself decays and collapses," he tells Delenn. "If the Narns stood in one place, and hated, all at the same time that hatred could fly across light years and reduce Centauri Prime to ash." She points out that the Centauri don't have to respond in kind (a vain hope since they started it) and he blames physics: for every action there is an equal and opposite reaction. While it doesn't impact the plot in this double episode, it's a reminder of the wider politics and that there are other, quieter conflicts still going on.
And that's it for this episode. Lots of loose ends, to be tied up in the next.