Three young girls are recruited to become test pilots for the new Sonic Diver program.

The girls travel to the military base and are introduced to each other and the other base personnel.

After all the girls have flown their Sonic Divers, it's their first pay day, and first day off. They meet a new friend, Takumi Hayami.

The girls learn to fly as a team. Otoha has trouble with the shooting practice.

Elise survives the destruction of the West Europe base. Back at Oppama base, Otoha finds a large bra and MUST find the owner. And the girls have a surprise in their combat simulators.

It's time for the girls to debut at the Oppama Air Festival, and they need a team name. The prototype fighter plane, the Vic Viper, debuts and its pilot causes the girls difficulties.

Fun and trouble at the local hot spring. The girls learn the truth about the Sonic Diver program.

The girls learn how to perform the "Delta Lock", a combat maneuver which traps the enemy WORM into a field where its cells collapse and can be destroyed. They also experience their first combat with a real WORM. Karen gets shot down and suffers a concussion and sprained arm.

The girls chase down rumors of a ghost on the base.

The girls meet Elise, a Sonic Diver pilot from the destroyed West Europe base.

Karen schedules a meeting with her older brother, but must miss it when she's called on a rescue mission. The Sky Girls team is moved from the base to a special-purpose ship called the Koryu.

The Sky Girls team settles into its new home at sea. Ryohei becomes seasick, preventing him from working on Reijin. When a WORM approaches the ship, Otoha is unable to launch, until Ryohei overcomes his illness and repairs their Sonic Diver.

The Sky Girls battle as a group of four for the first time but Elise, occupied by vengeance, has problems working together as part of a team. Vic Viper is involved in its first battle against a WORM, albeit briefly.

The military's strategy against the WORMs and their plan for the Sky Girls is made clearer. The Koryu is ordered towards a supposed location of a nest of WORMs. Eika's Father faints from over working. Eika's past is somewhat revealed as well.

The Koryu docks at a small island, which happens to be Nanae's home. Nanae is reunited with her childhood friend, Kurosawa Hiroharu, but lies about her job when he displays hostilities toward her ship. He finds out when a WORM attacks, he's saved by the Sky Girls.

The Girls become stranded on an island in the south Pacific and have to battle internal fissures that have not fully healed until they are rescued.

A new smaller WORM invades the Koryu.

Elise is suspicious of Aisha. The Sky Girls learn the origins of the WORMs.

Takumi finds some camera film. Otoha and the crew get to know Aisha. A new faster WORM attacks.

A Vic Viper squadron attacks a WORM with a self-recovery ability. Togo's backstory is also further explained.

Koryu holds a Christmas party celebration. A portion of Otoha's first encounter with WORMs is further revealed. A WORM in the shape of Otoha's long-lost brother makes a dramatic appearance.

Otoha deals with the ramifications of her brother having been resurrected by the WORMs.

The crew of the Koryu prepare themselves for their last battle with the WORMs.

All five Sky Girls and the Vic Viper squadrons engage in the final battle against the WORMs' nest.

The story catches up on the Sky Girls' lives six months after the WORMs were defeated.