The show is full of well-acted characters with interesting stories that feel incomplete given the limited main and recurring cast.
WARNING: Spoilers are unmarked.
- Superhero fanboy John/Captain Iron from "Man of Iron, Woman Under Glass" is an adorably earnest kid who never grew up and does have some genuinely useful Bunny-Ears Lawyer talents and accomplishments. He was also kidnapped and experimented on by the Valhalla Sector at one point and is deeply traumatized by the very mention of them. He had the potential to be a good semi-regular, but dies in his first episode without it even being related to the Valhalla Sector.
- Michael from "The Ground … Sown with Salt", is a frightening Faux Affably Evil Godhood Seeker and Wasteland Warlord who has an arsenal of military weapons (including missiles), a Dark and Troubled Past, and an interesting but ultimately unhealthy relationship with his pregnant Morality Pet. He is a more interesting villain than most of the Valhalla Sector and Army of Daniel characters, but he still only gets one episode.
- Julie, Michael's girlfriend from "And the Ground … Sown with Salt". Her desire to atone for staying loyal to to the psychopathic Michael for so long, being pregnant with his child, and having some Silk Hiding Steel Action Girl moments could have made her an interesting member of the Thunder Mountain community, but instead she is written out of the show with a Heroic Sacrifice in her debut episode.
- Some fans dislike how Hero of Another Story characters Knowledge Broker Eddie and Heroic Bystander William from "To Sail Beyond the Stars" don't become recurring sources of information about the world outside Thunder Mountain. With his Knowledge Broker business of finding people across the country, his tracking of Valhalla Sector-related atrocities, and his interest in seeing civilization return, Eddie had the potential to recur throughout the whole series.
- Farralon from "City of Roses" is a (possibly self-trained) young scientist who is working on a vaccine for the Big Death (which includes getting volunteers sick with milder forms of the disease to test their reactions). He is working for the Valhalla Sector but was in communication with Simon, who trusted him enough to tell him about Thunder Mountain. Farralon could have either been developed as an Unwitting Pawn of the Valhalla Sector who got a Heel–Face Turn or someone who knew exactly what he was doing and used the Thunder Mountain colony's trust in him to strike at the faction. Instead, he disappears after "City of Roses" except for a short flashback scene.
- Villainous Old Soldier Major Quantrell (Michael Rooker) from "Firewall" is probably the most interesting Valhalla Sector loyalist in the show by far. He has a richly bitter dynamic and Back Story with Markus and the other original Thunder Mountain survivors, being the former executive officer of the base, who abandoned them and is willing to kill them in the present and ends up as their Defiant Captive (which could have made him an Evil Counterpart to Meghan, another secluded, older resident of the base). He also knows Jeremiah’s father Devon and Ezekiel from his time at Raven Rock and is heavily implied to have bad blood with them (at least on their side) that is never fully explored. Consequently, it can be disappointing that he only gets one appearance.
- One of the last flashbacks in "Firewall" shows Markus taking charge of lots of children of the original Cheyenne/Thunder Mountain personnel in the aftermath of the Big Death, but during the main series, most if not all of Markus's named allies are people who started out elsewhere and were brought to the facility later. Their reactions to their old protector turned enemy Major Quantrell returning in "Firewall" and Markus hiding Meaghan's existence from them are never shown. Furthermore, some of these kids were young enough for Markus to have a Promotion to Parent role in their upbringing, providing another reason to lament how they only have background roles in the present.
- "Journeys End at Lovers Meeting" features an unnamed town leader who is committed to the survival of his town during a hard winter and is fairly resourceful (he got two cars working) but is also a Jerkass and The Social Darwinist, with a us-vs.-them mindset that makes him a Villain of the Week. He could have been a good Distaff Counterpart to Theo and either joined Daniel in season 2 or had some interesting Teeth-Clenched Teamwork with Jeremiah and Kurdy if he joined the Western Alliance, but he remains a One-Shot Character.
- Kwame, the leader of the Crescent Shadows black militant group, is a wary but ultimately reasonable potential recruit to The Alliance in his debut but, like so many similar characters, never reappears. It would have been especially interesting seeing him take a role in the Western Alliance and work to find a balance between doing the right thing for everyone and preserving the culture and values of his community while joining a government with white and interracial groups.
- Some people are surprised about how Erin's estranged twin sister Lauren doesn't show up in season 2 after she and Erin had some neat interactions together and began to reconcile after a long estrangement in Lauren's debut and how the emergence of Thunder Mountain and its alliance-building would give Lauren more reasons to seek out Erin again and more information about how to find her.
- Michelle from "The Mother of Invention" is the leader of a non-hostile community and has a rich history with Jeremiah (who may be the father of her son), but is only in one episode and doesn't even appear during later meetings of faction leaders.
- Bunny-Ears Lawyer Wylie from "Things Left Unsaid Part 2" is a hilarious but surprisingly ingenious character who solves the various mysteries of season 1 and then seemingly escapes from a trap where Jeremiah is captured. He could have become a big part of the Western Alliance in season 2 (especially given how Jeremiah moves to Wylie’s hometown) helping with the opening Rescue Arc and transition into fighting Daniel, but instead he's never seen again.
- Libby is introduced as an accomplished scientist and loyal friend to Devon (who is trying to undermine the Valhalla Sector from within). However, after the fall of the Valhalla Sector, she doesn't exert any scientific expertise or leadership skills and merely serves as a Satellite Love Interest and Love-Interest Traitor who dies without ever being confronted by Jeremiah and before her real motivations can be explored during a time where the plot had more than enough going on to let her do something more dynamic. Her status as the only female character to ever be in the opening credits (albeit only for half of season 2) makes her limited role in the plot all the more notable.
- Wicked Cultured Faux Affably Evil Valhalla Sector collaborator Davis and his lieutenants from "Strange Attractors" seem to get a Mook Carry Over after the Western Alliance runs then out of Millhaven and they talk about joining the Army of Daniel. Their knowledge of Millhaven (which Jeremiah is put in charge of running) and feud with the main cast could have made them interesting recurring Sims subordinates, but they are never seen again.
