The battle continues to rage as Ranban's troops try to break through the Royal Army's barrier. Ranban takes charge of the search for Aoi himself, and sends Mutsuki back to the Dainagon for doing exactly what her father did before her: not arresting an important criminal when he had the chance. Meanwhile, repairs continue on the Chunagon, but it's going to be a while before it's ready to fly. Despite everyone (and I mean everyone) piling on top of her, Mito dons her mail suit to out and look for Aoi.
As she waits for her punishment, Mutsuki thinks back to when she was just a little girl (and Masatuski was a baby), and the time she spent with her dad, when he told her that his job was protecting the galaxy's harmony. She hopes Aoi will be safe, but that's not a given with Ranban's forces on the loose. It's a wonder Aoi was able to stay hidden while unconscious (from the blast he produced in the previous episode). In order to get back to his mom, he climbs the side of a cliff, which fortunately for him gives him a direct view of the shielded Chunagon being fired at. Realizing he can't get close to the ship, he falls off the cliff, and only an opportune tree branch keeps him from falling into the Galactic Patrol's clutches. Somehow he finds a cave to take shelter in and ruminate on how he can't really do anything except make blasts that knock him unconscious, when suddenly, his mother appears! Aoi gives her a hug, but realizes just a little too late that it's unhelmeted Ranban, and not Mito (man, those identical mail suits!). Ranban kisses him on the lips, sending Aoi to sleep (it's not elaborated on, but I'm guessing there was some kind of tranquilizing lipstick involved). As rehelmeted Ranban takes Aoi into his transport ship, Masatsuki begs him to be lenient on his sister. Ranban promises nothing, but as he turns to leave, Sabu leaps into action! Her attack is a ruse, however, to let Shin sneak up on Ranban and Masatsuki. Ranban, however, has enough power to actually send her flying, and on top of that, actually harm her (and Masatsuki). While his enemies are down, he takes off in the transport ship posthaste, leaving Masatsuki behind. Mito arrives just in time to grab onto the ship and sneak onto the Dainagon that way.
Aoi's classmates have also been captured, and Mutsuki is the one to bring them their food. Although she dons the official Galactic Patrol mask to keep from being recognized, they recognize her voice anyway. And when an ill-timed mushroom pops her mask off, Kafuko does some quick styling, making Mutsuki's hair just like it was in her human disguise. But even though her secret is out, she can't go against the Galactic Patrol and help them, and when her friends push her too hard about Aoi, she runs off without even changing the freeze-dried students (and Miss Okubo) back to normal. As she leaves, she sees the ground troops have returned and asks about Aoi. They tell her that he was captured, and she feels better knowing he's safe, until she notices that Masatsuki wasn't with the rest of the troops.
Aoi wakes up in a circular room, and is immediately engulfed in flames, making him relive that flashback we all know and love. It's actually an experiment, and although the flames aren't real, they're extremely lifelike. Ranban has the scientists raise the level, and Aoi emits enough power to endanger the ship. Regardless, Ranban has the experiment continue. Eventually, Aoi destroys the room and the controls for the experiment, and passes out. Ranban concludes that he has found the true seal at last.
Unconscious, Aoi sits in a white plane, remembering things (only one memory is new footage) and feeling sorry for himself. He is approached by the shadow of his father, and the two embrace. Meanwhile, Mutsuki tries to get someone to help her find Masatsuki, but protocol keeps everyone at their post. During her search, Ranban has Aoi, still unconscious, wheeled to another room. She approaches Ranban, but is slapped away by one of the guards. Ranban says nothing, and Mutsuki heads off with determination. At the same time, the Galactic Patrol issues an ultimatum to Mito on the Chunagon, unaware that it's actually a shape-shifted Shin, and unaware that Masatsuki has been taken into the Chunagon's custody. The real Mito, to get further on the Dainagon, leaves her mail suit behind as a decoy.
Alone, Ranban exhults to the not-actually-there Mito that he now has taken everything from her: the galaxy, the seal, the royal sword, and even her son, whom he is keeping naked in his private quarters. To further enjoy the moment, Ranban desuits and then rages against the mirror and Mito, claiming she could never understand the curse he lives under, hating himself but still being forced to live (by whom?). He's just about to kill Aoi to spite Mito when the pirate herself arrives.
Episode Twelve - Our Seal/Waga Inrou!
Mito and Ranban banter for a few moments, then Mito runs to Aoi's naked body, only to find that it was just a hologram, a trap set by Ranban. He starts getting philosophical on Mito, commenting on how they are mirror images of each other (um, not really), as are their lives. And then he flashes back to his 10,000th birthday, when it was revealed that he is neither man nor woman (but had been claiming to be male), and thus he was imprisoned, went insane, and staged a coup d'etat by blowing up his home planet. Mito was away at the time, so she survived, and was happy to let Ranban rule as long as he was a fair ruler, but if not, she vowed to go pirate on his ass. As the flashback ends, Ranban reveals that he has the true seal this time around.
Back on the Chunagon, repairs are slowly but surely being completed. Carson finishes the repairs to bridge, but is told to avoid the engines, since his species can't take the heat, so to speak. Masatsuki, nearby for some reason, laughs at Carson's apparent uselessness. It looks like Carson's going to silence Masatsuki for good, but he instead frees him and tells him how to escape. Masatsuki can't go without knowing why a rebel would help a Galactic Patrolman, so Conrad tells him about how Masatsuki's father saved his life. He was once on the Galactic Patrol, but defected and was labeled a pirate. Trapped in the pull of a black hole, he was rescued by Colonel Nenga. Masatsuki realizes that this was the incident that disgraced his family's name, but rather than be upset about it, he's overjoyed that his father honored his convictions over his duties as a patrolman, and starts helping out with repairs to the ship.
Mutsuki finally reaches her determined destination, and frees her former classmates so they can help her save Aoi. They crawl through the ducts to the real room where Aoi is being held (still naked), and crash through the ceiling, with most of the girls landing on Aoi. Kafuko is bewildered by Aoi's apparent girl parts, and another girl who isn't named is bewildered by his lack of man parts. The boys cover Aoi with a sheet, but don't seem to notice (or keep quiet about it if they do). Their crash landing did not go unnoticed, but there are too many of them to escape without help. They need to contact the pirates!
In the dreamscape, Aoi gets a pep talk from his dad, who keeps emphasizing that Aoi needs to save Mito, not the other way around. Then he disappears, and Aoi wakes up, to the relief of all his friends. Now fully dressed (and apparently not caring or not aware of his sudden boobs), he leads the charge through the Dainagon, executing karate moves that he didn't even know he knew. As they race to the communication room, Aoi feels another shock like he did before, but stronger than before.
The Chunagon is finally ready to get back in action, and leaves the protective shield, wiping out all immediate enemy forces. Aoi is able to contact them, and Masatsuki and Mutsuki are reunited, kind of. To help Aoi, Sobo uses her royal command to merge the Chunagon with the Dainagon, and the crew rushes in to do whatever they can to help their cause. Sabu and Shin neutralize the troops going after Aoi and the others, and Masatsuki and Mutsuki are reunited for real this time. Although faced with the safety of the Chunagon, Aoi goes back into the fray, and Mutsuki follows after him. The other boys are prepared to fight, but Miss Okubo stops them.
Mito and Ranban have been fighting all this time, saber to saber, but Ranban uses his helmeted suit to detain Mito while he enters his mail suit. It looks like Ranban has the advantage, but he slashes through a wall that leads Mito directly to her own mail suit, evening the odds. Ranban still believes he has the advantage because, being neither male nor female, he has powers Mito does not, and even in six months, the wound in her shoulder hasn't completely healed. He manages to knock Mito out of her mail suit, just as Aoi finally makes it to them.
Episode Thirteen: Seize the Happy Ending!/Ryakudatsuse yo. Daidanen! (Let's Pillage. Grand Finale!)
Mito's crew do as much damage to the Dainagon as they possibly can, and manage to bring down the forcefield around the town. But while all that was going on, the Galactic Patrol's enormous Galactic Cannon was approaching, and now it's set its sights on Earth! Meanwhile, Aoi grabs Mito's light saber to fight Ranban, but gets another shock. Ranban, however, doesn't plan on killing Aoi, since Aoi himself is the seal, the switch that powers the royal sword. But that doesn't mean, he won't play with Aoi a little, and slaps him around with the light saber, all while boasting about how Aoi is powerless without his bracelet, an enhancer that brings out his powers. Despite hearing this, Aoi goes forth to protect his mother, and emits a blast of energy so powerful that it blows him and Ranban straight through to the top of the ship, without the bracelet. Ranban can't fathom how this could be, but Mito sets him straight: the enhancer was really a limiter, and now Aoi's powers have been unleashed unchecked!
Ranban proceeds to lose it, slowly advancing on Aoi while spouting nonsequiters about being left behind and the mirror looking at him. He and Aoi fight for real, with Mito's crew cheering Aoi on from the top of the ship, and his classmates doing the same from the Chunagon. Aoi slices off one of the mail suit's arms and begs Ranban to just surrender already. But by then the Galactic Cannon is lined up with the Dainagon, and Ranban teleports away. He shoots a beam directly at Japan, surrounding everyone with a dark light. A second beam starts powering up, and if no one stops it, Earth will be destroyed!
Sabu takes off with Mito and Aoi, and Sobo guides them to the launching pad for the royal sword. Once there, Aoi is flung into the system and suspended in the air while the starting sequence boots up. Mito tosses him the bracelet, but when he puts it on, he gets another shock. Ranban fires, and Mito activates the sword, but it doesn't work, due to Aoi's sex not being determined. Sobo explains to Aoi's classmates how their species doesn't become male or female until they become adults, and Shin figures that up until then, Kagerou's genes dominated, so Aoi was male. Sobo suspects foul play on Ranban's part, but that's neither here nor there, as Aoi has to become a definite gender or the Earth will be destroyed. Mito tries to get his hormones flowing by making out with him, but since she's a. his mom and b. looks like a little kid, it doesn't work. But Mutsuki might be able to do it...
With the beam from the Space Cannon drawing ever closer, Mutsuki kisses Aoi ever so gently on the lips and the controls suddenly spring to life! The Dainagon transforms into a giant sword, and a model sword appears in front of Aoi that he uses to control the Dainagon like Mito controlled the Chunagon a few episodes ago. He slices the cannon completely in half, and it explodes just like that. The Dainagon goes back to being a ship, and Aoi falls as his bracelet breaks. In the dreamscape again, he finds himself in his house, and his father thanks him for protecting Mito. He bids his father farewell.
Meanwhile, Mito's crew hastily carries the unconscious Aoi to the Chunagon. Mito explains to Mutsuki that she made Aoi the switch for the royal sword so Ranban wouldn't kill him if he ever captured him. She knew that Aoi's powers would activate some day, because her genes would dominate eventually, and gave Kagerou the bracelet to give to Aoi if anything happened to him. But when Kagerou knew his end was coming, he gave it to Aoi early, telling him it was an amulet. During this exposition, they reach the Chunagon, and Mito takes over as captain. The Chunagon disengages from the Dainagon, which sinks into the ocean. Aoi wakes up, and Mito embraces her son, a touching scene that leaves no dry eye on the Chunagon.
Later, all the freeze-dried humans are turned back to normal, and any survivors of the space cannon are rescued by the Royal Army. This includes Ranban, who asks to be killed, now that his grand plan has been destroyed. He excuses himself by saying he just wanted to get back what he lost: status, the galaxy, and Mito. Masatsuki steps up to the plate for Ranban, begging Mito to spare his life because he was a good leader. But Mito never planned to kill him, so it's all good. There's still just one matter to be cleared up, and Aoi's classmates take it on themselves to clear it up: Aoi is indeed a female now. Mito doesn't care whether she has a daughter or son, and Mutsuki is okay with shoujo-ai, but the rest of his classmates are not so cavalier about it, and Aoi is definitely not okay with it.
Regardless, Aoi is crowned Queen of the Galaxy, mainly because Mito didn't want to do it. Ranban drives off with most of the Galactic Patrol to points unknown, and Aoi follows his lead and takes off on his own in the Shonagon to try and find his missing manhood. Mito has Mutsuki and Masatsuki take charge as they follow after him, and the series proper draws to a close.