At a Nergal research lab on Earth, scientists are experimenting with “boson jumping”- teleportation through a chulip. Using a chulip secured in their lab, they send a manned Aestivalis through, with the aim of sending him to Jupiter. Unfortunately, the pilot does not survive the jump, but Erina is adamant that Nergal must continue the research. After all, the Nadesico survived a boson jump from Mars to Earth, so somehow, it must be possible.
Such weighty concerns are far from the minds of the Nadesico crewmembers, however. Christmas is just around the corner, and everyone is in a festive mood- whether it’s putting up decorations, organising a party, or just looking forward to getting off work early. Of course, in true Nadesico style, nothing is straightforward; despite the fact that Akatsuki has already invited everyone to a party, Yurika has arranged one of her own, whilst poor Seiya has just spent hours building the ‘ultimate party facility’, not realising that no one will be showing up to use it.
Not everyone wants to go to a party, though. Megumi would rather spend her Christmas alone with Akito, although when Ryoko hears this she decides to get to Akito first. Locking himself in his quarters, Akito watches Gekigangar under a blanket, hoping that he can hide out until they go away.
Another shipboard romance is going a lot more smoothly, however. Although they have kept it quiet up until now, Minato and Goat have been dating, and now they cannot help but share a kiss under the mistletoe. Goat has something else to give Minato- a release of her contract. At first Minato thinks that Goat is just paranoid about mixing work and pleasure, but Goat hastens to explain. The crew of the Nadesico are about to be drafted into the military- the missions will be dangerous, and the crew will no longer have the freedom to back out or pick and choose orders. It may be safer for Minato to stay on Earth.
Landing at a UEAF base, the crew is given a briefing explaining that the military doesn’t want a battleship under its command that is manned by civilians. Taken along with the cost of paying off the damages caused by the computer malfunction, it has become necessary to employ a military staff to run the ship- so if the current crew wants to stay on, they’ll have to be drafted into the military.
Akito isn’t too sure if he wants to become a soldier, but Munetake tells him not to worry- the military doesn’t want him, as a pilot or a cook. A trained pilot, Seelie, has been assigned to take his place- she will replace him on the Nadesico whilst Akito goes back to a civilian life on Earth (under surveillance, of course).
And if Akito is going, then Megumi is leaving too. Yurika wants to second that, but Akito tells her to stay behind- and when Megumi pulls him away, Yurika has no choice but to let the “happy couple” depart.
Wandering through town, Akito tells Megumi that he’ll probably go back to cooking now, even though with his nano-implant he’ll be stigmatised as a washed up pilot. Ironically enough, to Akito, it seems like no one wants him, but nothing could be further from the truth. In fact, even as he talks to Megumi, Erina shows up, with a new job offer that Akito just might be interested in.
Taking them to the research facility, Erina and her team, which now includes Inez Fressange, explain about the chulip and the research into boson jumping. The Jovians have only sent unmanned weapons through the chulips, and the crew of the Crocus died when they went through, but somehow, the Nadesico managed to make it back from Mars via a boson jump. And if Earth could master organic boson jumping, then they would be able to send troops through to Jupiter and Mars, altering the course of the war in their favour.
Both Inez and Erina believe that Akito is the key to organic boson jumping. Erina shows him a chulip crystal- a small blue diamond shaped crystal that looks just like the pendant Akito’s father gave him. Akito lost the pendant on Mars, and Erina believes that he somehow used it to make a boson jump to Earth when the Jovians attacked the Utopia colony. Akito admits that he doesn’t know how got to Earth, and that the crystal was missing when he arrived- causing a delighted Erina to realise that he is indeed just what she needs.
Erina’s sales pitch is interrupted when the Aestivalis previously sent through the chulip returns- now little more than twisted scrap metal. Following Erina to the chulip room, Akito sees the wrecked Aestivalis and realises that Erina doesn’t want a co-worker- she wants a guinea pig. Unwilling to listen further, Akito and Megumi leave, although Erina is sure that, once he realises he has nowhere else to turn to, he’ll come right back.
But whilst Akito merely wants nothing to do with the experiments, the Jovians want to shut them down entirely. The probes that made it to their homeworld alerted them to Earth’s experiments with organic boson jumping, and in retaliation, they send something back through the chulip- a pair of mecha much larger than any Aestivalis.
For now, though, the trouble hasn’t touched the Nadesico; whilst the other pilots listen to Izumi’s bad jokes at the Christmas party, Minato tells Goat that she isn’t going to take the opportunity to leave- she would rather stay onboard than go back to being a secretary. The fun is cut short, however, when Ruri receives a report- the Jovians are attacking.
The hostile mechs are not only huge, they are also equipped with gravity blast cannons. Whilst Ryoko, Hikaru, Izumi and Seelie attack in land frames, Akatsuki takes to the air. Watching the action on the news, Akito cannot forget about his friends- he wants to help protect them. Megumi argues that he already has her to protect, but Akito cannot listen. He knows that he has an important role to play in this battle.
The Aestivalis pilots launch their attack, but soon run into trouble- every time they try to score a hit, their opponents just teleport out of the way. Finally, Seelie decides to try a new tactic. If she can attach herself to one of the mechs, it won’t be able to teleport anywhere without taking her along with it.
Watching the battle, Inez and Erina are horrified- if Seelie is caught in a boson jump, she won’t survive. And indeed, when the enemy unit makes it next jump, Seelie is taken along for the ride- only to be killed when the cockpit of her Aestivalis is crushed by the jump.
Despite her unintentional sacrifice, Seelie’s attack disabled one of the enemy units, leaving the others with only one left to fight. Having analysed the enemy’s moves from his aerial vantage point, Akatsuki figures out the Jovian’s jump patterns and tells the other pilots exactly where to fire each time it jumps. The tide of the battle seems to have turned in Earth’s favour- that is, until the Jovians reveal their final trump card. Their mech cannot win, so instead, it overloads it phase transition engines. In just a few minutes, the energy from the PT overload will vaporise the entire area.
Fortunately, just as Erina predicted, Akito has returned, and he is about to put his boson jump capabilities to the test. Taking a case full of chulip crystals from Erina, he boldly runs out onto the battlefield, to the amazement of both the pilots and crew of the Nadesico.
Running up to the enemy mech, Akito opens the case, flinging it away so that all the cc’s spill out over the enemy. Glowing with lines of energy, Akito uses the cc’s to open a dimensional gateway, and the enemy is sucked in- followed by Akito himself. Has Akito just sacrificed himself to get rid of the second Jovian?
The Nadesico crew certainly thinks so, and as everyone returns to their post, Megumi angrily condemns Erina as being responsible for Akito’s death. Akito is far from dead, however- as Inez explains, he jumped through time as well as space, and ended up on the Moon two weeks in the past. Since then, he has been signalling the Nadesico to be picked up, and has only just now been able to get through. Alive and well (much to everyone’s relief, especially Yurika), all Akito wants now is to be picked up.
Meanwhile, down in the hangar bay, Seiya oversees the collection of the other Jovian mech. Despite it apparently being an unmanned weapon, there seems to be music coming from inside, and when the maintenance crew open it, they see not only a cockpit, but some Gekigangar comics and a tape player playing the Gekigangar III theme tune. Just what does this mean?