The statuses of many minor characters, allies and enemies alike, are left unclear after their sole episodes.
WARNING: Spoilers are unmarked.
- The white power groups from the pilot and the various warlord factions further off that Michael mentions in the fourth episode are strangely absent during the conflict between the Western Alliance and Daniel in season 2, with no sign of them either fighting to stay independent or joining the Western Alliance. This is especially pronounced since a Deleted Scene from the pilot has the white power gang leader musing over his encounter with the heroes in an intrigued way.
- In "And the Ground … Sown with Salt", it is unclear if two prisoners who Kneel Before Zod and are enslaved (while others are executed) escape with the fleeing prisoners at the end, are away from the base on a scavenging mission (the primary purpose of the work crew slaves), or are still at the base when it is blown up.
- In "And The Ground ... Sown With Salt", Michael tells Jeremiah and Kurdy that there are four factions besides him and the Valhalla Sector they should worry about having a fight with: The Rocky Mountain Brigade, the Mitchell Gang, the Army of the South, and the Posse Comitatus group in Montana. None of those groups are ever mentioned again.
- In "To Sail Beyond the Stars", William is never seen again after he and Kurdy split up while running from the Burners.
- The Mook who Kurdy catches trying to lead a group of pilgrims into a trap in "Journeys End at Lovers Meeting", beats up, deprives of his stolen boots (miles away from town) and interrogates, is never seen or directly mentioned again afterward.
- In "The Touch", the fate of the murderous Wasteland Warlord and his enforcers aren't shown after his people learn of his crimes and stop listening to his orders.
- Many episodes show Jeremiah and Kurdy trying to recruit the leaders of various towns (such as a Black militant in Moon in Gemini and Jeremiah's former lover Michelle in "Mother of Invention") for The Alliance, only for those people to never be seen or mentioned again in episodes where different local leaders debate joining the Western Alliance or decide how it will be run.
- In "Tripwire", when Jeremiah, Markus, and Kurdy visit Danbury the second time, they see the broken glasses of Blind Seer Damien, who is nowhere to be seen as his boss nervously cuts ties with Thunder Mountain after having clearly been intimidated by the Valhalla Sector. Whether Damien was killed, kidnapped, or just beaten up to apply that intimidation is never revealed.
- Rasmussen from "Thieves' Honor" is still fighting Theo for control of Clarefield (albeit largely off-screen) as late as "A Means to an End", but in the very next episode, "Things Left Unsaid Part 1", Theo is comfortable walking around town and it is never mentioned whether her feud with Rasmussen ended with his death or exile or a truce.
- In "Things Left Unsaid Part 1", Valhalla Sector soldiers attack the Brotherhood of the Apocalypse (an order of monks who were helping track rumors the Big Death is returning) and shoot everyone they find. Jeremiah, Kurdy, Ezekiel, and a wounded Elizabeth escape, but it is unclear whether any of the Brothers (particularly the two with the most Exposition) do.
- In "Things Left Unsaid Part 2", Thunder Mountain informant Wylie is with Jeremiah when they are spotted and chased by Valhalla Sector soldiers, but while Jeremiah is captured, Wylie's fate is unrevealed.
- In "Things Left Unsaid Part 2", St. Louis leader Nathan is seemingly the most prominent and influential community leader allied with Thunder Mountain and is captured by the Valhalla Sector along with Markus, Erin, Theo, and many others. He is never seen again, even when the prisoners are being rescued and then debating about their new laws.
- Raymond Jaglom and the rest of the Thunder Mountain governing council, who are occasionally prominent in season 1, never get a mention in season 2.
- The last known remaining Valhalla Sector collaborators decide to join Daniel at the end of "Strange Attractions", but are never seen or mentioned again.
- Karl from "Voices in the Dark" and Frederick Monash from "The Face in the Mirror" are both high-profile defectors from the Army of Daniel who have lots of important information (Monash moreso than Karl), but are never seen or mentioned after the episodes that devote a lot of time to getting them to Thunder Mountain. This can feel especially odd for Monash, given how his status as one of the older remaining survivors of the Big Death would make him stand out at Thunder Mountain.
- The nomads who briefly shelter Dr. Monash in The Face in the Mirror are last seen being questioned by Sims, and it is unclear if he lets them go after one of them reluctantly tells him where to find Monash.
- At the end of the finale, the Founders, the leaders of Daniel's government, are exposed as the callous, manipulative Not So Well Intentioned Extremists they are, with this revelation coming while one of them is surrounded by angry soldiers, but it is never shown what punishment he faces, or if his three colleagues are also caught.
