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, 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 device 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 Atmosk; but she quickly retracts her offer reasoning that Naota is still "just a kid". Haruko takes Naota's and Atomsk fusion guitar 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, Naota and his friends have begun their junior high school year. Furthered with an a typical argument over drinks between Naota and Ninamori implying some minor signs of romance. As Naota seemed to have kept Haruko's guitar as a memento; whether he learned to play it or not is unknown. Naota finishes his final monologue up with the same first episode statement that contrasts the genre of the series "Nothing ever happens here". At the end of the credits, Haruko's vespa is seen parked at Naota's house.
Opening Song: Carnival
Kitsurbami gets sick: Funny Bunny
Manga scene: Come Down
Naota talking to Haruko: One Life
Mamimi feeds cellphones to Terminal Core: Another Morning
Mamimi feeds moped 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