There's a huge, giant hand looming over Mabase and the Medical Mechanica plant hasn't stopped smoking since the battle with the last robot. Both Haruko and Canti are wanted. Mamimi has found a new friend, a little robot that has a taste for eating mechanical things.
Haruko and Canti have disappeared and become wanted criminals, while smoke has continued to pour out of the Medical Mechanica plant since the last robot attack, shrouding Mabase in mist. Mamimi finds a small dog-like robot by the river. It runs away with her cell phone, which she lets it eat, and it grows as a result. Haruko returns to the Nandaba residence at dinner, causing Naota to later ask her in tears why she left. Commander Amarao and Lieutenant Kitsurubami attempt to find the "Terminal Core" of a robot they haul out of the river, which is revealed to be the creature Mamimi has been feeding. It absorbs part of Canti before Haruko feeds Naota to it, then drills into the giant hand. From this, Haruko hopes to extract Atomsk, the celestial being whose power she desires.
Before the giant hand can fully grasp the Medical Mechanica plant, Canti stops it as Naota emerges from his head, glowing with the infinite energy of Atomsk. Stunned, Haruko flies into a rage, bent on acquiring the power of Atomsk by destroying Naota. Before he can finish Haruko off, Naota stops short and declaring his love for her, kisses her, allowing Atomsk to fully emerge from his N.O. channel. Atomsk consumes the Terminal Core and blasts into space. Before leaving, Haruko asks Naota if he wants to accompany her on her search for Atomsk, but she quickly retracts her offer, reasoning that Naota is still "just a kid." Haruko takes Naota's and Atomsk's fused guitars, presumably keeping it as a memento, and zooms away towards the sky on her Vespa, leaving Naota to find her guitar lying among the rubble.
In the epilogue, life returns to normal in Mabase, a year has passed since Haruko left, and Naota and his friends have begun their junior high school year. There is a typical argument over drinks between Naota and Ninamori, implying some minor signs of romance. Naota kept Haruko's guitar as a memento in his room; whether he learned to play it or not is unknown. Naota finishes his final monologue with the same statement made in the first episode that contrasts the events of the series: "Nothing interesting ever happens here." At the end of the credits, Haruko's Vespa is seen parked at Naota's house.
Opening song: "Carnival"
Kitsurubami gets sick: "Funny Bunny"
Manga scene: "Come Down"
Naota talking to Haruko: "One Life"
Mamimi feeds cellphones to Terminal Core: "Another Morning"
Mamimi feeds mopeds to Terminal Core: "Beautiful Morning With You"
Kamon talking with Miyaji: "Nightmare"
Haruko says “It's the climax!”: "Last Dinosaur"
Naota has Atomsk’s power: "I Think I Can"
Haruko says goodbye: "Little Busters"
- Original Concept: GAINAX
- Executive Producers: Toshimichi Ohtsuki, Mitsuhisa Ishikawa, Hiroyuki Yamaga
- Planning: Hirotaka Takase, Masatoshi Nishizawa, Hiroki Sato
- Naota Nandaba: Jun Mizuki
- Haruko Haruhara: Mayumi Shintani
- Mamimi Samejima: Izumi Kasagi
- Kamon Nandaba: Suzuki Matsuo
- Shigekuni Nandaba: Hiroshi Ito
- Eri Ninamori: Mika Itou
- Gaku Manabe: Sho Miyajima
- Masashi Masamune: Kazuhito Suzuki
- Commander Amarao: Kouji Ohkura
- Kitsurubami: Chiemi Chiba
- Junko Miyaji: Yukari Fukui
- Miyu Miyu: Hideaki Anno (uncredited)
- Takkun: Jun Mizuki
- Naota Nandaba: Barbara Goodson
- Haruko Haruhara: Kari Wahlgren
- Mamimi Samejima: Jennifer Sekiguchi
- Kamon Nandaba: Joe Martin
- Shigekuni Nandaba: Steve Kramer
- Eri Ninamori: Melissa Fahn
- Gaku Manabe: R. Martin Klein
- Masashi Masamune: Steven Blum
- Commander Amarao: Dave Mallow
- Kitsurubami: L. Villa
- Junko Miyaji: Jessica Straus
- Miyu Miyu: Steven Blum
- Takkun: Barbara Goodson