The movie begins with Fuyuki Hinata and the Keroro Platoon exploring an abandoned temple in the mountaintop city of Machu Picchu in Peru. While on the exploration, Keroro accidentally sets off a trap, and by chance 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. As soon as the group realized what was happening, they run out of the room. While running, Keroro accidentally loses his Kero Ball while Fuyuki catches a fleeting glimpse of a glowing young woman as he is running out, and tells Keroro that there was 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... (Source: AniDB)

One day, a stone carving bearing an uncanny likeness to Keroro arrives at Fuyumi's place. To solve this mystery, the Keroro Squad travels to the isolated and mysterious Easter Island. There, they meet harmless spirits known as Mana, and the odd twins Io and Rana. Lastly, there is Akuaku, a legendary evil spirit recently awoken from its long sleep. (Source: AniDB)

What was the tragedy that decided the fates of Char Aznable, the man later nicknamed the Red Comet as an ace pilot of the Zeon forces, and his sister Sayla Mass? The two siblings' journeys, brought on by the sudden death of their father Zeon Zum Deikun who was a leader of the Spacenoids, are depicted in the four episodes of Chronicle of Char and Sayla. The Zabi family who seize control of Side 3 and lead the Principality of Zeon, the early days of many renowned Zeon ace pilots who later fight in the One Year War, the secrets of mobile suit development, conflicts with the Earth Federation Forces, and the road leading to the outbreak of war—all will be revealed. (Source: Official Website)

The first two episodes are summaries of the TV series, the third one (Crest of Iron) takes place in an alternate universe.