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...
Unfortunately the movie Sergeant Keroro The Super Duper Movie 3: Keroro vs. Keroro Great Sky Duel is not yet available on HBO Max.
| Writing | Masahiro Yokotani | Writer |
| Visual Effects | Toshihiko Fukano | Key Animation |
| Visual Effects | Yasuzo Iino | Key Animation |
| Visual Effects | Yuki Oomori | Key Animation |
| Visual Effects | Susumu Mitsunaka | Key Animation |
| Visual Effects | Hiromi Matsushita | Key Animation |
| Visual Effects | Toshiyuki Anzai | Key Animation |
| Visual Effects | Raku Nishikimi | Key Animation |
| Visual Effects | Kayoko Yabuki | Key Animation |
| Visual Effects | Masaki Inada | Key Animation |
| Visual Effects | Satoshi Hattori | Key Animation |
| Visual Effects | Shinya Uchida | Key Animation |
| Visual Effects | Shinji Nagata | Key Animation |
| Visual Effects | Miyuki Matsumoto | Key Animation |
| Visual Effects | Tsutomu Nishiyama | Key Animation |
| Visual Effects | Erina Kojima | Key Animation |
| Visual Effects | Masaru Yonezawa | Key Animation |
| Directing | Susumu Yamaguchi | Director |
