I met pulp author Van Allen Plexico at DragonCon a couple years ago and we're friends on Facebook. Earlier today, he posted this article, "The 'Missing Insurgency' of Babylon Five's Final Seasons."
The gist of it is that Plexico expected evil Earth leader Morgan Clark to have more popular support among the Earth Alliance population. His regime was not in power long and humans who didn't openly challenge the regime were likely left alone. Meanwhile, rebel commander John Sheridan, due to his alliance with the Minbari (who had nearly eviscerated the human race a little over a decade before) would perfectly fulfill Clark's propaganda against aliens and their allies. Given how Clark had taken control of Earth's media outlets, he had years to fill Earth's population's collective heads with half-truths if not outright lies about Sheridan and friends. Consequently, Sheridan and the White Stars should have faced a lengthy postwar insurgency even after their victory in the Earth Alliance Civil War.
I suggested that Clark's last-minute "Scorched Earth" attempt to turn the planet's defenses against the population would have been enough to absolutely discredit Clark, his regime, and anything associated with it. After all, shooting yourself and trying to take all of Earth's people down with you has a way of making everybody hate you. Furthermore, although anti-interventionists often claim that people will rally around a dictator against a foreign threat no matter how bad they are, the Italians in WWII greeted Allied troops as liberators even before Mussolini fell and the Germans came in en masse.
Plexico's response was that Mussolini had been misgoverning Italy for years and was in the process of losing a long war against the Allies, in contrast to Clark's regime that was only in power for around three. Furthermore, Clarkist die-hards could claim "Scorched Earth" was propaganda by Sheridan's allies. Considering how it took a lengthy space battle to neutralize Earth's orbital weapons, it does seem plausible that pro-alien traitor would claim Clark had intended to massacre his own population when his real goal was to cripple Earth's defenses for his alien masters.
I wasn't really familiar with Babylon Five even though I did watch Babylon Five: In the Beginning on television once and I remember the episode in which Sheridan's rebels raced against time to stop Earth's defense platforms from firing. I did a bit of reading and found that the worst of Clark's atrocities (i.e. mass killing, as opposed to just dissolving the elected government) took place off-Earth. This would explain why so many Earth warships, which would have faced a choice of committing war crimes or mutiny, defected to Sheridan's rebellion. However, with his control of the media, Clark could have deceived the people on Earth itself about the nature of his military activities abroad and the nature of the uprising. Consequently, even though most of the Earth Alliance would view Sheridan and company as heroes, there might be a large number of people on Earth who would think otherwise. Those people could be a problem later on.
A possible model for how this could have happened is Iraq in our history. The insurgency could consist of die-hard Clark supporters analogous to the Baathists, open followers of the Shadows analogous to Islamists (Clark was in league with them, but given his regime's xenophobia, I imagine this was kept quiet), and, for a touch of moral grayness, "Earth nationalist" rebels who disavow the horrors of Clark's regime but think Sheridan, the Interstellar Alliance, etc. are a subtle alien takeover of Earth.
You wouldn't even really need that many--a small crew of Clarkist fanatics or those still devoted to the Shadows even after they left the galaxy (think the human equivalent of the Drakh) could stir up trouble in hopes of provoking a crackdown by Sheridan's human troops or (even better) alien allies, which would vindicate them in the eyes of the people and attract more support. Heck, if the show wanted a sympathetic human foe, someone who means well but has been deceived by evil people and/or aliens (like the Shadows), simply wants to pull the Earth Alliance out of the Interstellar Alliance due to isolationism and lack of a Shadow threat, or was just really traumatized by service in the war with the Minbari and isn't thinking straight would work. It doesn't have to be a major plot arc--maybe a one-off episode where a bunch of PTSD-addled veterans of the Earth-Minbari War try to assassinate Sheridan or commit some kind of outrage on Babylon Five itself.
Thing is, Babylon Five ran from 1994 to 1998. The wars in Afghanistan and Iraq (especially the latter) were well into the future. Even the Kosovo War, which featured an Albanian insurgency that deliberately provoked the government to attack civilians, a thuggish Yugoslav government all too willing to be thuggish, and an international intervention that resulted in vast numbers of Serb and Romani (Gypsy) civilians fleeing possible Albanian reprisal, was still in the future. Although I could credit B5 creator J. Michael Straczynski with enough creativity to potentially come up with this on his own, the real-life incidents that would inspire such episodes and resonate with the viewer (think about how the Iraqi occupation inspired much of the New Caprica arc in Battlestar Galactica) had not happened yet.
It could still be a pretty cool story though.
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