The story picks up with the battle group fully formed, and the big wigs are planning the operation. Otoha is still having a very difficult time trying to operate her sonic diver unit, Ryohei tries to get her motivated but it doesn’t seem to work. Just as the admiral is getting briefed about the sonic diver team, a new island is discovered in front of the battle group, and everyone thinks that the island is the nest. A short while later the military headquarters reports that the worms have begun attacking major cites all around the world, so they must begin attacking the nest. The mission plan is for the ships to begin attacking the outside of the nest with the Vic Viper unit blasting a path to the nest’s interior, and then the sonic diver team will enter the nest find the core and plant the DNA virus. Aisha will pilot the new craft and Otoha will be left out of the mission because of her fragile mental condition, Togo tells the other pilots to keep this secret from Otoha. When Aisha is linked to her sonic diver unit her sync rate is over 100% and Eika learns that this causes Aisha to have complete memory loss when she is piloting her unit, and this is the reason for her lack of memory during their fist dogfight. Later the girls decide not to keep this a secret from Otoha, so the have a talk with her about comradeship, teamwork, trust and faith, they get her to agree to fly again.
Eika tells Togo that Otoha will fly with them and Togo agrees to get permission form the higher ups, Eika tells him that she’ll take responsibility for the mess, but Togo says what kind of commander wouldn’t trust his troops. Otoha begins to train extra hard to regain her sync rate with her sonic diver unit, and after a talk with Aisha she regains use of her sonic diver unit and rejoins the other pilots in the ready room. Then the final battle begins, first the battle group attacks with cannon and missiles, then the carrier’s jets attack attack followed by the Viper unit, and finally the sonic divers join the battle.
The battle with the worms causes losses on both sides, after a while Karen is able to determine the weakest location on the island so the Viper team clears a path for the sonic divers unit to enter the nest. After the sonic diver unit enters the nest the battle outside heats up, many ships and jets are destroyed fighting the worms, and the Viper unit destroys many worms. Inside the nest worms approach the sonic divers from the rear, Eika and Elise stay behind to fight them sending the other three girls forward to continue the mission. The Eika and Elise’s battle with the worms seems to be going badly, they are badly outnumbered but fight bravely, Karen must also engage worms on her own sending Aisha and Otoha on with the mission. Even the Koryu is heavily damaged during the battle outside the nest, but the crew struggles mightily to save the ship. A short while later Aisha and Otoha find the core of the nest and Otoha attempts to hold off many worms while Aisha tries to insert the DNA virus into the core. The girls fight valiantly while Aisha is inserting the virus into the core, Eika runs out of ammo in the battle, and the other units also struggle against almost hopeless odds.
When virus insertion reaches 100% the worms seem to go into a dormant state, but as everybody is about to celebrate victory the effect wears off and the worms come back to life. Togo orders a retreat because the mission is a failure, but before that happens the core opens reviling Otoha’s brother Yuuki, he greets her saying he has been waiting for her. Otoha loses her sync with her unit and falls into the water, the other girls are trapped by the worms while coming to her aid. Just then Yuuki and the core materialises a sonic diver unit and it begins to attach Aisha and her unit. At the last minute Otoha realizes the promise she made to everyone about being a team and rejoins the fight, Yuuki asks her if she’ll fight him and she says yes that’s what she came to do, and fight of her life begins. The worms attempt to absorb Otoha and her unit saying the world no longer needs humans, a short while later Aisha grabs Yuuki and tries to change him back into a human being. The transformation works allowing Otoha to destroy the worm’s sonic diver and Yuuki dissolves into light just as Otoha reaches him, he says thank you for keeping your promise.
After Yuuki disappears the worms start to deactivate and turn to dust all over the world, the nest starts to collapse around the girls. Otoha goes to rescue Aisha who’s fallen unconscious after her efforts changing Yuuki back into a human. The collapse of the nest stops and Otoha carries Aisha back to the outside where every one’s waiting for her. Well, that’s all for episodes 24-25, below are some screen shots.
Well it all comes down to this, the final mission, the last battle, even though a great deal of planning goes into the mission, a feeling of melancholy hangs over everything. The girls decide that even though Otoha is having great difficulties trying to regain her emotional ability to be a pilot they won’t let that break their bonds of fellowship with each-other and convince Otoha to fly again, they will fight together, and live or die as a team, this isn’t blatantly said but they all know it to be true. Even if all the mission planners want everyone to return safely all the key personnel knows that some might die, so many feeling are finally expressed out in the open for the first time. Otoha and Ryohei finally are able to somewhat admit their mutual attraction, and Gen (the ship’s cook) asks Elise if she wants to be adopted by him and his wife after the fighting is over, she accepts his offer since all her family and friends were killed earlier in the war. Karen and Takumi are also able to show mutual feeling towards one another, or at least Karen is able to look Takumi in the eye while she’s talking to him (hell maybe she’ll even be able to kiss him in ten years), and Eika and her father also reconcile their father/daughter relationship. When the battle’s joined everyone displays courage and self-sacrifice during completion of the mission, they never give up. In the end, Otoha is finally able to keep her promise of flying together with her brother, and it looks like the worms are finally defeated. From the preview of the last episode it looks like it will be a wrap up to the series set in the near future, look forward to it.