At a research lab, a boy stands in a room next to a dead girl on a bed and ponders the differences between humans and animals. Years later at the Battle of A Baoa Qu in December UC 0079, GM pilot Bianca Carlyle struggles to break free from a Bigro‘s claws before stabbing it through the cockpit with her beam saber. Zeon pilot Billy Hickam uses his Psycommu System Zaku to destroy multiple EFF targets simultaneously. Inside the space fortress, a Gundam Head team takes down Zeon resistance and clears the path for Creed and Sonia’s troop-carrying Guntank, which blasts a door open and deploys its troops. At Confeito, an EFF staff officer named Monica Humphrey wonders how the Zeon can’t even grasp the situation until the fighting ends. As a Chibe crashes into the surface of A Baoa Qu, Daryl pilots a Gelgoog and evacuates a pod carrying Karla’s medical capsule. He lands a few hits on some GMs, but his prosthetic hands struggle with the standard cockpit controls. A GM nearly kills him, but he gets saved by Fisher’s Rick Dom. A battered and naked Io rescues his comrades from imprisonment. After the battle ends, EFF special forces troops secure a manufacturing site where three additional Zeongs are under construction. Daryl and Fisher retreat to a Musai, which is carrying Io’s wrecked Full Armor Gundam. Monks fish through the debris and reclaim the bodies of dead pilots to cremate them. In August UC 0080, Luggun pilots Kate and Janice fly over the Sydney Crater and pick up several Medeas on radar, so they fire signal flares. A squad of Core Fighter pilots led by Barclay launch from the Medeas and turn to attack incoming Dopps. Inside one of the Medeas, Io listens to jazz from the cockpit of his new Atlas Gundam.
Daryl carries a radio as he walks on a beach and thinks about being a boy with all his limbs intact. Fisher works on his Acguy and complains about the heat, but Daryl is amazed by how beautiful Earth is. The team’s mechanics spray paint an emblem on Daryl’s Acguy to honor him as a survivor of the Living Dead Division. Billy and Sebastian Morse talk about how no one can match Daryl’s self-sacrifice and patriotism. At night, Daryl, Fisher, Billy and Sebastian head into the ocean with their Acguys. In space, the assault carrier Spartan begins atmospheric re-entry. Cornelius conducts maintenance on Bianca’s Guncannon Aqua, and she asks him about being a survivor of the Thunderbolt Sector. She wanted to see the famous Gundam, and Cornelius wishes that Io were here for this operation. As the ship travels through the atmosphere, Bianca unstraps from her seat to see the ocean from a window. She wants to get out and fight, vowing to crush any enemy in her way. An orbiting Musai launches a Komusai piloted by Julio and Gregory on a mission to kamikaze attack the Spartan. The Spartan fires its anti-air guns at the Komusai, and Captain Vincent Pike wants to fire anti-air missiles even though they can’t lock on. The Atlas Gundam launches from a Medea and uses a small fighter as a booster sled to ascend rapidly. Io then takes off and uses the thrusters on his blade shields to speed past the Spartan. He fires his railgun at the Komusai to knock it off course, then moves in close and uses his beam saber to slice the shuttle in two. On one of the Medeas, Monica declares that the Atlas Gundam will be essential for this operation. Io lands the Atlas Gundam on the Spartan‘s deck, and Cornelius is surprised when he hears jazz music. Below the surface of the ocean in a Mad Angler sub, a Zeon officer named Phillip Kaufmann vows to get revenge against the Federation.
Monica addresses the crew of the Spartan and notes that in addition to Zeon remnants, they also have to contend with the South Seas Alliance that is planning to break off from the Federation. The cult members in the alliance have obtained something dangerous: the Psycho Zaku, which Monica notes destroyed the Beehive, three Salamises and the Full Armor Gundam. The Zeon uses amputees to maximize movement synchronization, and Vincent is sure that the cultists would have no problem severing limbs for their beliefs. Monica explains that they’ve brought in the Atlas Gundam to destroy the Psycho Zaku before the cultists can use it. Bianca walks up to Io after the briefing and says that she likes the song “Groovy Duel” that he was listening to as he landed. They both boast about being able to play without mistakes, so later on they play a duet with her on the keyboard and him on drums. Kaufmann wakes up in a drunken stupor on the Mad Angler and has his bottle taken away by Lt. Bull. He cries about how he and his wife had to pull their six-month-old son’s body out of rubble. After the Spartan takes off, Bianca watches as some team members get tattoos. She takes off her shirt, revealing multiple tattoos from her many assignments. Vincent tells Marie that she’s clear to launch on a patrol mission. Io and Bianca talk about how jazz has developed in the UC. Bianca suggests they should play “Groovy Duel” with no mistakes if they survive this next battle. The four landing craft take off from atop the Spartan and deploy Ball Marine Types to search the icy waters of Antarctica. Kaufmann takes off in a Gogg from the Mad Angler. Ball pilot Carolina is surrounded by glacier fragments and is then killed by the Gogg. The landing craft launch their GM Marine Types, which dive underwater and are attacked from above by Z’Goks that shoot glacier fragments and cause them to sink in the water.
Bianca launches in her Guncannon Aqua and sees the GM Marine Types being crushed by glacier fragments. She spots the Mad Angler below her and opens fire on it, but Kaufmann deploys freeziard to dispel her attacks. He then slashes into the Guncannon Aqua with his claws, and she stabs the Gogg with a beam saber. The two jump onto the surface, and Kaufmann slices off Bianca’s right hand. Io launches in the Atlas Gundam and heads for the battlefield on his support craft. As the Gogg and Guncannon Aqua slide across the ice, Kaufmann tells Bianca that he won’t pity anyone in the Federation, even a woman. Bianca quickly changes some energy settings and activates both sabers for a blast through the Gogg’s torso, and she uses her feet to flip the Gogg off of her. She then fires a missile at the Gogg, and both suits eventually roll to a stop. She doesn’t want to wait for her energy to recharge and grabs a handheld machine gun. Bianca walks out on the ice and finds the Gogg cockpit empty. She sees Kaufmann in the distance with some penguins and targets him with her scope, but she stops when she hears the loud steps of a Z’Gok approaching from the rear. The Z’Gok moves to smash her and is sniped by Io. He destroys multiple Z’Gok’s with his railgun, but three units counterattack by binding the Atlas Gundam with Luna Titanium chains. Io tries to break free by jumping, and he fires sticky material out of his shield that stops all three Z’Goks. He then rams his railgun through one of the Z’Gok’s and fires to destroy all three units. One lone Z’Gok escapes, but Io gives chase. The blade shields combine with his shield to form a sled, and Io boasts about how the Atlas Gundam is amphibious. Io dodges the Z’Gok’s attacks and stabs it with his beam saber for the kill. He then comes under fire from Bull’s Grublo and barely dodges its mega particle cannon. Bull fires a barrage of missiles at Io, and the cloud of bubbles allows Bull to get close and grab the Atlas Gundam. Io fires his rifle as the mega particle cannon charges, but he runs out of ammo. Io manages to break free at the last second, but takes damage to his legs. He then stabs the Grublo and causes water to flood into the cockpit. The Grublo sinks and implodes when the pressure becomes too great. Io sinks as well and can’t use his leg thrusters, so he uses beam sabers to propel himself. However, the beam sabers stop working, causing him to sink again. As the Atlas Gundam sinks, Bianca’s Guncannon Aqua grabs it and pulls it up. Bianca tells Io that they saved each other and are even now. Kaufmann returns to the sub and says a silent prayer for Bull. On the Spartan, crew members mourn their many losses from the battle.
Daryl follows Karla as she playfully explores a forested area. The two enjoy food with an older couple before leaving. Karla wants to enjoy the natural honey that the old people gave them and refers to Daryl as “daddy.” They leave the forest and return to the interior of a submerged Dolos ship hidden in the ocean. Due to the psychological trauma that Karla experienced at the end of the One Year War, she has mentally regressed to a child-like state. Because her father was also missing a hand, she has come to associate Daryl with him. His task is to help her recover her memories so that the Reuse Psycho Device can be recreated by the Zeon remnants. A female officer wants Daryl’s field work to be limited due to this project, but she’s told he has other duties. Daryl returns to work on his Acguy, which is being fitted with custom equipment for his next mission. Daryl’s Acguy team deploys in a Jukon sub that launches from the Dolos. On the Spartan, Io and Bianca complain to a mechanic about the slow repair process on the Atlas Gundam and Guncannon Aqua. Cornelius grabs Io by the ears and teases him for wrecking a new mobile suit. On the Jukon, the team reviews the mission plan, which involves their Acguys infiltrating the South Seas Alliance to recover a Zeon spy. Daryl’s team, which includes Fisher, Billy and Sebastian, launches from the Jukon. Elsewhere, the Spartan deploys its weapons, Core Fighters and GM Ground Type-Cs on its landing craft. Bianca and Io remain on standby since they have no mobile suits to launch in.
The Acguy team reaches land, and Daryl deploys reconnaissance equipment to update his map of the area and send it to his men. The Acguys begin their march. In the South Seas Alliance territory, the Zeon spy moves through the city as people stop everything to pray. The Zeon team encounters villagers in a small hut, and an Acguy gives chase when a girl tries to run away. The Acguy activates its heat hawk and accidentally sets a tree on fire. The girl then escapes and fires a signal flare. South Seas soldiers arrive and open fire as the spy reaches the forest. Several South Seas Dahle suits arrive and open fire on the Acguys. A group of South Seas Goufs flying on Dodai YS units surround the Spartan. Daryl’s team fights the Dahles while he searches for the spy, but he comes under attack and is knocked into a waterfall. The attacking Dahle pulls out its beam saber and moves in on Daryl. A woman identifying herself as Commander Peer demands that the Spartan fall back immediately. Io and Cornelius are shocked when they recognize the voice on the radio. Io examines a Core Fighter’s visual feed on one of the Dodais and is shocked to see Claudia’s face.
Io runs through the Spartan, and Bianca corners Cornelius and asks about the woman, so he tells her that they thought Claudia was dead. Pike tells Claudia that they’re on a mission to clear out Zeon remnants and rudely demands that she get out of his way. A Gouf fires its bazooka as a warning shot, and Pike orders the spread of Minovsky particles. Daryl opens fire on the Dahle and destroys it. He finds that now he can’t regain the signal on his map for where the spy is. Io prepares to launch in a GM Ground Type-C and asks Bianca to support him with a Corvette Booster flight unit. The Spartan opens fire on the Goufs, and one of the Dodais fires missiles that knock out the ship’s optical and heat sensors. Daryl’s men ask him to order a retreat because they’re running low on ammo, so he gives the command. Billy has a Newtype reaction and tells Fisher to shoot in a specific spot. Fisher fires a missile at the area and destroys several Dahles. Daryl’s Acguy is knocked into the water after he picks up the spy. A Gouf is destroyed at close range, damaging one of the ship’s cannons. Monica tells Pike that it was a suicide attack to make way for its allies to approach the ship. The Gundam Ground Type-S team tries to counter incoming Goufs with hover units, including one piloted by priest Chow Ming, who praises High Priest Levan Fuu as he attacks. Soldiers with jet packs disembark from the Gouf’s hover unit and storm the Spartan. Water unit-equipped Dahles ride the river and give chase to Daryl, who speeds through the ruins of a submerged city. Gundam pilot Orphe attacks a Gouf with a beam javelin and slices into it with a beam saber. Chow Ming tries to attack him with a bazooka and is hit from above by Io’s GM. Io kicks the Gouf as he lands on the deck and knocks it off. Io then jumps onto the Corvette Booster to chase down Claudia’s Dodai. A Gouf gets close to the Spartan and is destroyed by Creed and Sonia’s Guntank. Creed prepares to switch to hand-to-hand combat and tells Sonia she can stay in the cockpit if she wishes. Billy decides to hang back and see if Daryl is actually a skilled pilot, or if his accomplishments were due to the Psycho Zaku. The Spartan‘s soldiers trade fire with the cultists, and Pike notes that they aren’t numerous or well-trained. Monica wonders if they have some objective other than invasion. Io jumps onto a Dodai to see if Claudia is in the cockpit, and he shoots it when he confirms that she isn’t. He jumps back to the Corvette Booster, and Bianca tells him that jumping on every Dodai is insane. He says he wants to find out what happened to Claudia, and Bianca tells him that she might’ve been brainwashed by the priests. A cultist sets off a grenade as he dies, damaging the outer hull. A wounded cultist staggers into the Gunperry hangar and gives a pouch to an EFF soldier who bears the cult’s tattoo, and the soldier shoots him in the head.
Daryl notes that the enemy has stopped attacking and thinks that something is wrong. Io grabs onto another Dodai, which attempts to shake him off. Bianca fires a missile at it, and he shoots it with his machine gun. They then destroy another Dodai when he sees that Claudia isn’t on it. Daryl speeds toward a damaged bridge and deploys frizzy yard to protect himself from attack as he jumps in the air. A Dahle grapples onto him, but he rams a spike through it and kills the pilot. Daryl falls into the water, and Billy destroys a damaged Dahle attempting to attack Daryl. The Acguy team then speeds along the river and deploys explosive balloons in the water to stop the enemy pursuit. Io and Bianca destroy another Dodai and come under fire from the one that Claudia is in. He jumps off his Corvette Booster and lets his beam saber be destroyed by their machine guns to create a blinding flash. Io opens his cockpit and demands that Claudia say his name, which she does. However, Chow Ming wraps his shock wire around Io’s GM and pulls him off the Dodai. The Gundam pilots watch over Io’s GM after it returns to the ship. Cornelius asks about Claudia, but Io tells her he needs to talk to Monica. She reveals that she knew Claudia was with the cultists, which is part of the reason why Io was brought on for this mission. Pike asks about an item found in Monica’s room, and she explains that it’s an incense container she gave as a farewell gift to children who left her Newtype laboratory. The Zeon spy shows shows Daryl a picture of Sexton, who is now with the South Seas Alliance. Monica explains that Levan Fuu’s brain was severely damaged from long-term experiments conducted on him, so he developed telepathic abilities that allow him to control his cult followers. Monica says that she raised and abandoned Levan Fuu, and that he’s a Newtype. Elsewhere, Levan Fuu telepathically controls his followers as they pray in front of the Psycho Zaku.
The Bandit Flower compilation movie combines the four episodes that comprise Gundam Thunderbolt‘s second season. Compared to December Sky, the amount of new scenes for this compilation are minimal. The most notable additions are a new opening scene with young Levan Fuu, Io being tied up while fighting Z’Goks, and Creed and Sonia using their Guntank during the South Seas Alliance attack. Due to the minimal additions, Bandit Flower suffers from some of the same issues as the individual episode versions, namely, that a lot of material from the manga is compressed for time. Also, even with all that compression, the story ends just before major manga developments occur with the Spartan invading South Seas territory and engaging in major battles. It’s not clear when there will be additional Thunderbolt anime, but the manga contains more than enough material for two more seasons/movies. If that ever happens, hopefully they would be more substantive adaptations than Bandit Flower.