This one's a monster of the week episode, and while it doesn't do as much heavy lifting as Soul Hunter it still manages to set up some key themes for the show.
First up, there's a reporter on the station. She's been trying to get an interview with Commander Sinclair for Babylon 5's second anniversary, and he's been avoiding her. "He'll grab any chance to take out a ship," she complains to Garibaldi. I'm honestly not sure what she's doing in this episode, as all she does is chase Sinclair for a statement and generally make a nuisance of herself, but I guess they needed a B plot. Since this episode works perfectly well without her it's possible this contributes to the perception of Infection as the weakest episode of the season (according to Wikipedia).
The A plot involves Doctor Franklin, who's now settled in and gets a visit from his old xeno-archaeology teacher. Doctor Hendricks wants help figuring out some artifacts he picked up during an excavation of Ikarra VII. They appear to be some sort of organic machines, which the Vorlons are known (and the Minbari rumoured) to have. Both Hendricks' employer Interplanetary Expeditions and biotech will feature in later episodes. What the viewer knows and Franklin doesn't is that the artifacts have been smuggled onto the station and not been through quarantine. Hendricks' assistant Nelson killed a customs officer to get them in, rather than pay the bribe the man was rather obviously angling for.
This willingness to kill causes the artifacts to bond with Nelson, turning him into a bioweapon designed to protect Ikarra VII. The catch? The weapons were programmed to protect the planet from anyone who wasn't a "pure Ikarran", and once the invasion was over turned on their creators - because no one is pure anything. Ikarra VII is a dead world.
Nelson goes on a rampage, powering up in incremental levels that will destroy Babylon 5 in a matter of hours, and after several failed attempts to stop the weapon with violence Sinclair decides to try to talk it down. In the end he persuades it to look at Nelson's memories of Ikarra VII. Realising it has ultimately failed in its purpose, it shuts down.
After the fight, Garibaldi comes to see Sinclair. He feels the commander is taking too many risks, in a way he's seen before in veterans of the Earth-Minbari war - particularly those who were in the Battle of the Line. In fact he tells Sinclair he's putting himself "on the line" too often, phrasing that can only echo back to what he feels is the source of the problem. And he's right, although not for the reason he thinks. Sinclair is initially offended at the implication he has a death wish, but admits Garibaldi has a point.
Meanwhile, Franklin and Ivanova have an after work drink and muse on the notion of racial purity. Franklin's heard rumours of a pro-Earth movement back on Earth that's committing hate crimes against aliens, and is worried about the future. I don't think it's a coincidence the characters having this conversation are both members of groups with a history of being persecuted, a black man and a Jew. The only thing that stops this being completely heavy-handed (although the rest of the episode isn't subtle by any means) is that it hasn't been revealed yet that Ivanova's Jewish. In the middle of the conversation soldiers from Earthforce arrive to confiscate the weapon, showing Franklin is right to be worried.
In the end Sinclair finally meets with the reporter. She asks him if going to space is worth it, or should humans pull back and deal with their own problems on Earth. It's worth it, he tells her, because even if for no other reason one day the Earth will be destroyed and all of humankind's achievements with it. While I understand this is probably Sinclair playing politics, and thinking about all that was lost on Ikarra VII, for me it's a Human-centric response that undermines the rest of the episode.