When Garibaldi is describing the weapon used on Isogi, Sheridan asks if it was a Slaver's Glove. This weapon was previously seen in Born to the Purple (1994) in Season 1.
When asked why he chose San Diego as the site of a terrorist attack, executive producer J. Michael Straczynski said that he had once lived in the city, and, "You write what you know."
When Taro Isogi meets Amanda Carter, a Mars government representative, he tells her, "I can very well imagine that's what they said of your great-grandfather John when he volunteered to pilot the very first colony ship to Mars." This is a reference to the character John Carter of Mars, the initial protagonist of the Barsoom stories by Edgar Rice Burroughs who made his first appearance in the 1912 novel "Princess of Mars".
Bureau 13 has its headquarters in "The San Diego Wastelands". The city was destroyed in a terrorist nuclear bombing, which Commander Sinclair mentioned in Midnight on the Firing Line (1994) (1.01).
When J. Michael Straczynski found out that Bureau 13 was an RPG (role-playing game), he promised never to use it in a story again.