Fuyuki Hinata and the Keroro Platoon are exploring an abandoned temple in the mountaintop city of Machu Picchu in Peru. While on the exploration, Keroro sets off many booby traps, and they find a hidden chamber with a large blue crystal in the center, on a stand that has a key in it. Keroro leans on the key, causing the room to activate a mysterious machine, this caused the entire temple to shake. The platoon run out of the room when they see this. While running, Keroro accidentally loses his Kero Ball and Fuyuki catches a fleeting glimpse of a glowing young woman as he is running out, and tells Keroro that there is a girl in the room, but he is forced to leave the room before he can say anything else. The group successfully escapes, while the girl (now sprouting a pair of glowing wings) watches them leave - while back in the chamber, something is growing within the crystal.
It moves on to the movie's official title sequence (making this the first Keroro movie to actually have one).
The story continues back in the Hinata household, where Natsumi, Koyuki and Fuyuki talk about Macchu Pichu. Natsumi almost drinks a mysterious bottle of fluid, when Keroro saves her at the last minute, as the bottled drink was actually a type of weapon drink called "Nanola", whatever the liquid touches turns into a terrifying weapon of destruction. Fuyuki then reminds Keroro that a new Gundam model has arrived at the toy store (possibly the Gundam Master Grade RX-78-2 Ver. 2.0), however, Natsumi told him that he still had chores to do. To cheer his friend up, Fuyuki said that he would buy the new Gundam for Keroro, overjoyed from Fuyuki's kindness, Keroro gives him his wallet to use for the Gundam.
Meanwhile, an unknown group was watching them. The leader was quite disturbed by Keroro's lack of leadership, and decided to relieve him of his duty of invading the planet. At the same time, Momoka called the Keroro Platoon over to have them answer for an unknown installation on her family's super computer. They stated that they weren't responsible, but then, a soldier reported an unknown object coming rapidly towards them.
After Fuyuki finishes buying Keroro's Gundam, everyone living in Tokyo witness an enormous ship appearing out of the sky. The Platoon runs outside the Momoka mansion to meet the invaders. The first is Shivava, a cocky Keronian who says he is a Great Sage Surpassing Heaven, who makes Tamama envious. The second to appear is Doruru, the trainer of the first Keron Army that Giroro served with. The two invaders reveal that they aren't working for the Keron Army, but instead were working for another Keroro, this one darker than the original, Dark Keroro. He arrives in a darker version of the Keroro Movie Mecha to declare himself the new king of the world. He proceeds in telling the platoon of the current situation, his domination of the world in 2 minutes. During the first minute, he took control of all the economy and super computers on earth, he then proceeds to the market, the military, and so on, that made one minute complete. In the second minute, he sends greeting cards to all the world leaders, and immediately sends his Mini-Keroro robots across the globe, to land and send out hypnotic waves to brainwash all who reside in the area, including Natsumi and Koyuki.
However Fuyuki arrives, shocked after seeing everyone in town acting strangely. Dark Keroro was surprised, as Fuyuki seems immune to it but isn't worried, since he is planning on the Giant Keroro Statue, a weapon said to be the ultimate destroyer. Dark Keroro then jumps into his Dark Keroro Mech, then proceeds into attacking the group, as well as Fuyuki. After the onslaught, Dark Keroro and his followers leave for their ship, without knowing that Keroro is following them by hovership. Meanwhile, Mois, unaffected by the waves, arrives to help Fuyuki take care of the other platoon members, while those who ARE under the waves control are working on parts of the Giant Keroro Statue. Fuyuki then leaves to help Keroro by using another hovership while Mois helps the battle-damaged platoon members, Giroro wakes up in time to hear from Mois what has currently happened, then Dororo arrives to tell them what happened to their friends.
Fuyuki arrives atop the ship to see a wondrous view of the cities that lie on top; the hovership he was on broke down and was plummeting down, then he was saved from falling by an angel-like woman named Nasca, the same woman he saw in Machu Pichu. After Fuyuki and Nasca parted, Fuyuki found a passage inside the ship. Giroro and Dororo were trying to get through to Koyuki and Natsume, who were already under the control of the Mini Keroro's hypnotic waves, but nothing happened, Tamama wondered why they weren't under the wave's control, and Dororo said that it was because they were Keronian, and a Keronian weapon can't affect other Keronians. Mois said that neither her or Fuyuki were under the Mini Keroro's control, thus raising the question as to how that's possible.
Somewhere in Dark Keroro's ship, Keroro and Fuyuki reunited, only to be washed away by the tide of water that goes through the underground hall, Fuyuki and Keroro were then saved by Keroro's hovership, just in time for their friends to arrive and help. They were then ambushed by Shivava, and then afterwards, imprisoned in the ship's barrier by Miruru, the ship's system operator. Doruru arrives to blow the group out of the sky while Kululu is forced to deal with Miruru. Doruru succeeds in shooting them down, forcing Dororo to catch them all on his shuriken hoverboard - the resulting overload causes him to crash-land in what appears to be a colosseum.
When Fuyuki, Mois, and the Keroro Platoon regain consciousness, they find Koyuki and Natsumi preparing to fight each other, due to being under Dark Keroro's hypnotic weapon's control. Kululu then reports to the platoon that Dark Keroro is a clone of Keroro, grown from a sample of Keroro's DNA off the Kero Ball, enhanced by super carbon and educated in a different way then Keroro was. After the discovery, they witness Koyuki and Natsumi's mindless battle with each other, this forces Giroro and Dororo to fight their friends and try to save them. While the friends were fighting each other, the answer to why Fuyuki and Mois were immune to the hypnotic rays was revealed, Mois's wrist protector which keroro gave her and the wallet that Keroro gave Fuyuki to buy the newest Gundam, are Keronian items, thus giving the one in possession of the item complete immunity of the hypnosis weapon. Keroro and Fuyuki told Giroro and Dororo about the Keronian items, and told them to place one of their things on Natsumi and Koyuki. Giroro throws his trusty bandolier on Natsumi, while Dororo throws his ninja knife on Koyuki's shoulder pad: these items freed the two girls from the mind control.
The entire group makes a run for it (though Giroro has to be carried away as he is rendered helpless without his bandolier), but were cornered by Dark Keroro and his subordinates. Fuyuki takes a gamble on Dark Keroro's similarity to Keroro, and tries to distract him by throwing Keroro's new Gundam model into the air: the plan falls flat as Keroro himself runs after it. Shivava unwittingly blasts a hole in the ground of the colosseum; Keroro and the others made their escape through the hole, then evade the pursuing Shivava when Fuyuki triggers a convenient trapdoor beneath them.
The kids (Fuyuki, Natsumi, Koyuki and Mois) and the Keroro Platoon rest for the coming battle. Tamama and Giroro in the meantime were wondering if they could defeat Shivava and Doruru, then Mois and Natsumi gave them words of encouragement that gave them hope for their rematches with the two soldiers. At the same time, the everpresent mind-control problem is rectified when Giroro hands Natsumi his bowie knife and takes back his bandolier (and returns to full form as a result), while Dororo simply exchanges knives with Koyuki.
A few hours later, Kululu made an astonishing discovery, apparently, the Keronian weapon Kiruru, the same weapon that threatened the planet twice (it used people's negative emotions against them in Keroro Gunsō the Super Movie, and then possessed Meru in Keroro Gunsō the Super Movie 2) was threatening the planet once again. As it turns out, Dark Keroro is actually the 3rd generation of Kiruru. The first Kiruru was created for enemy alienation, whereas the second was made for destruction, the third and final one was made for one thing, and one thing only, absolute rule.
While the team was planning on how to defeat the third Kiruru (Keroro actually resurrects his rather harebrained scheme from the 2nd movie, involving everyone dressing up as princesses), an army of bracelets attached themselves to each one of them, and with a bright light, they disappeared from each other's sight. The bracelets were revealed to be Dark Keroro's newest weapon, the "Super Anti-Barrier", the wearer can neither hear or see other persons wearing the bracelets. Dark Keroro then separates them, planning on them to lose hope and become lost and alone forever, however, Kuyuki and Dororo don't need to see each other, they have been through events like this before and could easily sense each other's presence. While separated from the others, Fuyuki met with Nasca once again, only to be brought to Dark Keroro's throne room.
In the meantime, the rest of the group were still trying to look for each other, when Giroro wished for a weapon, Natsumi thought of the same thing, as did the rest of them. Nasca was revealed to be Miruru all along in disguise. As Miruru left, Dark Keroro proceeded in inviting Fuyuki to join him as his soldier, but Fuyuki declined. Confused, Dark Keroro threatened Fuyuki to join because he demanded it, causing Fuyuki to state "If that's the only way you can get others to submit to you, then you are not a king!" This angers Dark Keroro even more, so he gives a direct order to Shivava and Doruru to find and kill Fuyuki's friends, but Shivava and Doruru declined the order as well, they even told him to shut up.
Meanwhile, still concentrating on the group's thought of a weapon, Keroro ran straight to his Gundam model in the colosseum, where everyone else came, they all still couldn't see each other, but it didn't matter to them, they knew that they were together, and in celebration of finding each other, they built the Gundam together, forming a complete Mobile Suit action figure. Keroro then proceeded in pouring some of the Nanola on the Gundam, changing it into a giant robot, just like the giant mechs in the Gundam franchise. At the same time, Kululu and Natsumi finished work on an entirely new weapon, the Mini Kululu, thousands built with the technology to negate the Mini Keroro's brainwashing waves, and restore the people of earth back to normal, and freeing Momoka and her military squad as well. Keroro pilots his new Gundam robot straight at where Dark Keroro is, at the same time, Miruru uses the ship's defenses to attack the Gundam, blasting whole pieces off of it, until Koyuki and Doruru destroyed the combat system within the ship, causing everything to break and go haywire. Keroro blasts into the ships main building and is told by Kululu that Fuyuki and Dark Keroro are on the above floor. Keroro points the Gundam's beam rifle up and shoots a hole in the ceiling (This scene is a reference to a scene of the final episode of Mobile Suit Gundam when Amuro Ray and Char Aznable were battling).
With the Gundam reduced to a mere Core Fighter (the Gundam's cockpit fitted with its own propulsion system, like a minijet), Keroro finally made it into the enemy's throne room. As Fuyuki was trying to get Keroro out of what was left of the Gundam, Dark Keroro tried to convince him that it was pointless to try to save him, however, their bond was too strong for Dark Keroro to understand, and Fuyuki pulled Keroro out of the ship. Just when they started to rejoice, Dark Keroro screamed and summoned his Dark Keroro Mech to destroy both Fuyuki and Keroro. Dark Keroro is now determined to kill Fuyuki, seeing this coming, Keroro places Fuyuki inside the Gundam cockpit, knowing that he should be safe. Dark Keroro then focuses on killing Keroro, but before he could land a punch, something came out of nowhere and punched HIM. It was Keroro's own mech, the original Keroro Mech, remote controlled by Natsumi to come straight to Keroro's aid. The two mechs fight each other, leaving Fuyuki concerned about Keroro and what would become of him, as the battle progressed further, Keroro seemed to have the upper hand, until Dark Keroro shot one of his mech's arms off, giving Dark Keroro the perfect opportunity to attack, when suddenly, Fuyuki came in the way of Dark Keroro's deadly attack by ramming the Dark Mech with the Core Fighter.
The Dark Mech crashed and Keroro claimed victory. Dark Keroro called Shivava and Doruru for back-up, but he was rejected again. Dark Keroro then fell into despair, he had no one to help him, and no weapon to use, Keroro wanted to negotiate a cease-fire, but Dark Keroro refused, knowing that no one would obey him, he then set off a switch that made the Super Anti-Barrier glow even brighter, when Fuyuki opened his eyes the first thing that he saw was gunfire, gunfire that came from Keroro's mech and destroyed the Dark Mech completely, he even blew Dark Keroro into pieces. Keroro was speaking like a deranged villain, he even said that he would kill Fuyuki, his friends, and destroy the entire planet; terrifying as it is, Fuyuki wasn't buying it, he knew Keroro wouldn't crave for blood, so Fuyuki uncovered the truth, that wasn't Keroro at all, it was an illusion. The fake Keroro dissolved into nothing as the real Keroro emerged, free of the illusion; the successful resistance to the Super Anti-barrier destroyed the bracelets that were attached to the others.
Dark Keroro couldn't believe that they overcame his Super Anti-barrier's illusion, Keroro and Fuyuki were convinced that Dark Keroro was as rotten as they come, and could never be forgiven. However, Dark Keroro had one more trick behind his sleeve, The Giant Keroro Statue. The Statue parts have gathered together and the group could only watch as it is pieced together piece by enormous piece. However, the ship itself is a piece to, the tipping causes everyone to fall off, including Keroro, Fuyuki tried to save him but it was too late. The others are rescued by Momoka, Kululu and Natsumi, and they witness the completion and raw power of the Keroro Statue. The kids and the platoon prepare for the final battle, as Giroro and Tamama are confronted by Shivava and Doruru, Koyuki and Dororo deal with the Statue's defences. Dark Keroro and Fuyuki view from the top of the Statue to witness the strength of Fuyuki's friends, Dark Keroro started losing it, he questions Keroro about the bond that he and Fuyuki have, and Keroro told him that there was nothing special, and then Fuyuki said "Caring for friends is something that's shared by all, including humans and invaders." Dark Keroro still couldn't understand, and then, an explosion from one of Momoka's military ships blew off a piece big enough to crush Dark Keroro, but before he could meet his end, Fuyuki and Keroro protected him by shielding him from certain death.
Back in the aerial battle above, Tamama is unable to gain any edge over Shivava, until he snaps into full psycho form and lets loose with all his dirtiest tricks - from farting into Shivava's face to ganging up with Momoka and clobbering him into submission; Giroro defends a battleworn Natsumi by charging at Doruru and risking a barrage from Doruru's own Dendrobium mecha, until Natsumi returns Giroro's bowie knife and he shoves it into Doruru's weapons, allowing Giroro to defeat him.
Dark Keroro finally started to understand Fuyuki and Keroro, and blamed himself for everything that happened, they told him that Kiruru is to blame, not him, so Dark Keroro decided to go alone and stop Kiruru, and then Miruru appeared, it turns out, Miruru is the key to seal away Kiruru, just like Mirara from the First Movie. Miruru warns Dark Keroro that if he does succeed in sealing Kiruru, then Dark Keroro himself will disappear, he didn't care, but Fuyuki did, before Dark Keroro continued, Fuyuki told him that they could be friends, hearing that made him happy enough to save Fuyuki's planet. Dark Keroro seals away Kiruru, and disappears, along with the Keroro Statue, everything fell apart, Fuyuki could only watch as a good friend lost his life for a small planet. The sun rises, and Fuyuki and Keroro stand in the rubble where the Giant Statue used to be, but to their amazement, Dark Keroro was alive and well (his normally red eyes now black, and with an afro to match), it seems that he didn't disappear because the part of him that was a king died, while the other, lived as a friend.
The end credits:Dark Keroro is given a Little Comet spaceship (from the series) to make his departure with, and he bids farewell to his new friends.
Keroro and Angol Mois dig through the rubble and recover their Kero Ball and Lucifer Spear respectively.
Shivava takes part in an intergalactic martial arts tournament; we see him defeating an opponent, who's wearing a familiar-looking orange jumpsuit with a black belt...
Doruru digs himself out of the rubble, alive and quite well; he is later seen using a rocket booster (which resembles the G-Armor module from classic Gundam) to head into space.
The Garuru platoon make a cameo appearance, picking up the Miruru-key and taking it back to Keron.
Dark Keroro decided to see the universe, see other planets, and meet friends like the ones he met on Earth. Shivava and Doruru follow him to a new Earth-like planet, where a parody of episode 1 occurs, but with a few 'alien' touches.
Sergeant Keroro, Dark Keroro - Kumiko Watanabe
Corporal Giroro - Jōji Nakata
Lance Corporal Dororo - Takeshi Kusao
Private Second Class Tamama - Etsuko Kozakura
Sergeant Major Kululu - Takehito Koyasu
Fuyuki Hinata - Tomoko Kawakami
Natsumi Hinata - Chiwa Saitō
Momoka Nishizawa - Haruna Ikezawa
Mutsumi Saburo - Akira Ishida
Koyuki Azumaya - Ryō Hirohashi
Angol Mois - Mamiko Noto
Nazca - Saki Fukuda
Doruru - Ruu Ooshiba
Shivava - Minami Takayama
Miruru - Yui Horie
Aki Hinata - Akiko Hiramatsu
Paul Moriyama - Keiji Fujiwara
556 (Kogoro) - Nobuyuki Hiyama
Lavie - Tomoko Kaneda
Practice soldier - Kenji Takahashi
Announcement - Taro Masuoka
Crew - Seiro Ogino
Pilot - Tomoaki Maeno
Mother - Yumiko Akaike
Woman A - Shion Hirota
Woman B - Yukiko Matsuyama
Woman C - Yoko Hikasa
Boy - Uncredited
Child - Uncredited
Older sister - Uncredited
Younger sister - Uncredited
Amuro Ray - Tōru Furuya
Theme song: Arienai Kurai Kiseki (ありえないくらい奇跡, Impossible Dark Miracle)
Artist: Ayano Tsuji; Beat Crusaders, Label: Speedstar Records
Opening theme: Kero! and March 2008 (ケロッ!とマーチ 2008, Kero! to Māchi 2008)
Artist: Teruyuki Tsujima; Kanako Yanagihara, Lyricist, Composition, Arrangement: Kan Sawada, Label: flying DOG; JVC Entertainment
Moeru! Keroro (燃えろ! ケロロ, Burn! Keroro)
Tobe! Gundam (翔べ!ガンダム, Tobe! Gandamu)
The film included a 17-minute short named Musha Kero: Debut! Sengoku Planet Ran Big Battle!! (武者ケロ お披露目!戦国ラン星大バトル!!, Musha Kero Ohirome! Sengoku Ran-sei Dai Batoru!!).