With both Akito and Inez now down in the ruins, Erina knows that Yurika won’t be trying to destroy them any time soon, and both the Kakitsubata and its Aestivalis units break off the attack. All they and the Nadesico can do for the moment is wait and see what happens.
Making their way down into the ruins, Akito and Akatsuki still have quite a way to go before they reach Inez- and with distortion fields blocking their way every 800 metres, the going is slow. Akatsuki wonders just who Inez wants them to see, but recollections from memory mah-jongg soon provide Yurika, Ruri and the pilots with an answer- it must be Ai. For the sake of those crewmembers still in the dark, Ruri gives a quick explanation about how Akito met the girl before his boson jump to Earth, and has since experienced a great deal of pain and anguish over her apparent death.
Ai is far from dead, however- she is down in the ruins with Inez, waiting for Akito. Inez listens as Ai explains what happened to her- her mother’s death, the attack on Mars, and how she accidentally got caught in Akito’s boson are all described from her childish perspective.
The Nadesico, meanwhile, has other problems. A free-falling Jovian chulip has just landed on Mars, and in short order, a Jovian ship emerges and attacks the Kakitsubata. The ship is the same one that first attacked the Nadesico with the boson cannon, and Captain Genhachiro looks forward to a rematch with the ‘dashing man of action’ in charge of the Nadesico.
Down in the ruins, Inez requests an update from Megumi, who explains about the appearance of the chulip. Inez realises that the presence of the chulip is accelerating the ruins’ activities, but before she can say more, the transmission is cut off, and the Nadesico finds itself in the midst of a battle with the enemy ship and its robots.
The accelerated activities mean that Ai will soon be boson jumped away again, and glowing lines of energy appear on her body even as she clings to Inez in a futile attempt to stay. Realising the Akito won’t get there in time, Inez tells Ai to be strong- there will come a time in the future when she will get to meet Akito, and until that time, she must be strong and never forget about him. Agreeing that she will always remember Akito, Ai hands over a small section of metal plate before disappearing again.
Akito has finally made it to the bottom of the shaft, but as he jumps out of his Aestivalis, Inez tells him that he is too late, although maybe that was meant to be. With the transmission to the Nadesico restored, Inez explains her part in the story- she and Ai are the same person. When Akito first boson jumped to the Earth, Ai jumped with him, but as she was unable to visualise Akito’s destination, she got lost and ended up on ancient Mars instead. The people who built the ruins sent her back to this time and place, but when the Jovian chulip triggered the ruins to make her jump again, she ended up in the Martian desert twenty years in the past. Found by Nergal researchers, Ai became Inez, and grew up with no memory of her past- until the memory mah-jongg unlocked them again. Finally realising the whole story, Akito apologises, and a tearful Inez collapses into his arms.
On the Kakitsubata, Erina is less interested in Inez’s story than in getting some help against the Jovians. The Jovians have concentrated their forces against the Kakitsubata, and Nergal’s newest warship cannot take the strain. Under Akatsuki’s orders, Erina and her crew abandon ship, right before the Jovian robots blow it up.
Back on board the Nadesico, Akito and the Howmei Girls are sitting by the unconscious Inez’s bedside. As the Howmei Girls try to convince Akito that what happened to Ai/Inez was not his fault, Yurika watches from the doorway, before turning away and leaving.
As the Nadesico descends into the ruins, Genichiro sends them a message. Their safety can be guaranteed only if they surrender and allow the Jovians to take control of the ruins- something Yurika has no intention of doing. Neither Earth nor the Jovians can be allowed sole possession of the ruins.
Still lost in her grief, Minato remains alone in her quarters, watching Gekigangar. As she muses over how Tsukumo could have been taken with what is essentially a very flimsy and shallow show, Yukina interrupts her. It is time for Minato to stop feeling sorry for herself and live up to her responsibilities- which includes honouring her promise to become part of Yukina’s family.
Meanwhile, Yurika has unveiled her plan of action to the Nergal and senior crew members. She still wants to destroy the ruins, and it looks like the best way of achieving that is to blow up the Nadesico, once everyone except Yurika herself has evacuated. Eavesdropping from outside along with the rest of the main crew, Akito bursts in when he hears this, determined to dissuade Yurika from her suicidal course. Yurika is adamant that her plan is the best way to end the war, and the conversation degenerates into an argument, at least until Seiya interrupts with some interesting news. According to Inez, destroying the ruins could undo all the boson jumping that has ever occurred, literally rewriting the course of history.
As the crew ponders this, another interruption occurs as a familiar face enters- Admiral Fukube. Inez found him in the ruins, where Jovian grasshoppers were holding him as a prisoner of war. Fukube tells them that self-destruction is out of the question, and Ruri agrees. Undoing the past would mean losing all the memories and experiences they acquired aboard the Nadesico- a price that no one seems willing to pay.
Instead, the crew come up with a different plan- instead of destroying the ruins, they will bring the unit that controls boson jumping aboard the Nadesico. As Megumi and Ruri supervise its retrieval, Minato finally reports for duty. Yukina helped to snap her out of her depression, and now Minato is determined to keep it together for her new ‘family’.
Under Kusakabe’s orders, Genichiro orders the Jovians to attack, and Genhachiro leads a team of five Gekigan type mecha into the ruins. Ryoko and the other pilots offer to hold them, giving the Nadesico enough time to execute its plan. Standing together on the observation deck, Inez, Yurika and Akito will boson jump themselves, the ship and the ruin computer far away from both Jovian and Earthling hands.
Unfortunately, the initial attempt at boson jump fails. Inez concludes that the only way to create a large enough jump field is for two of the boson jumpers to make membrane-to-membrane contact- and the easiest way to do that is for Akito and Yurika to kiss. Surprisingly, Yurika refuses to do it, and Akito’s suggest that they just grit their teeth and endure it only makes matters worse- causing Yurika to boson jump away by herself.
Fighting the Jovians together with the other pilots, Akatsuki finally realises that it is only those people who are born on Mars who can survive the boson jump process- the ruins’ computer must have programmed the Martian nano-machines to rewrite their DNA in order to allow it. And now, one of those Martians- Yurika- is using that ability to jump all over the ship, with Akito following right behind her!
Yurika finally jumps into Akito’s Aestivalis, and to everyone’s surprise, she is able to control it thanks to a nano-machine implant that she seems to have just acquired. On Inez’s advice, Akito jumps into the Aestivalis with her, and the two fight for control of the robot. Unaware that their conversation is being broadcast to every ship within range, Yurika and Akito begin to argue. Yurika tells Akito she wanted to turn back time because of his guilt over what happened to Ai, but to Akito, it is just another of her crazy schemes.
Finally, the pair calm down, and Akito tries to explain his feelings. He finally watched the last episode of Gekigangar, and despite the fact that it turned out to be a poor episode, something in it appealed to him. There is a part of him that wants to believe in the simple ideals of Gekigangar- perfect good and hot-blooded passion, and, as Yurika surmises, it is that part of him that also loves Yurika. After a satisfied giggle at hearing Akito finally admit it, Yurika tells him that she loves him as well- and another argument ensues as Akito insists that this is the first time she has actually said that, whilst Yurika argues that it can’t be. Finally, the argument is ended with a kiss, and with the required contact made, the Nadesico finally makes its successful boson jump.
The story has come to an end, and it is left to Ruri to wrap things up as best she can- which isn’t very well, given the self-confessed number of loose ends still remaining. Yurika and Akito’s love story may have finally been wrapped up (and for now Ruri has to wonder if kissing was strictly necessary for the actual boson jump), but as to the identity of the ancient Martians, the meaning of the plate that Ai gave to Inez, or even the outcome of the war (not that either side will have the inclination or ability to carry on fighting without the boson jump unit from the ruins at stake), well all that will have to wait- until the inevitable sequel comes out.