It's the late 22nd century, and the Jovian lizards are attacking Earth. Nergal Heavy Industries decides to build its own battleship, the Nadesico. Captained by the ditsy yet tactically brilliant Yurika Misumaru, and crewed by an bunch of misfits, how will the Nadesico fare in its first battle against the Jovians?

Not liking the idea of a powerful battleship in the hands of civilians, the United Earth military sends Admiral Misumaru's fleet to take control of the Nadesico. Will Yurika be able to protect her ship from her own father? And will Akito ever find out the truth about his parents' deaths?

The Nadesico's next destination is Mars, but in order to get there, it has to pass through the Earth's various lines of defense, including the Big Barrier. Can the Nadesico convince the United Earth forces to take down the barrier, or will they just have to defy Earth and punch their way through?

The Nadesico heads out to the L2 colony to pick up some new Aestivalis pilots, but end up on a rescue and retrieval mission of a more urgent nature after the colony is destroyed in a surprise attack.

On the long and boring trip to Mars, Mr Prospector insists that Yurika take the time to perform funerals for all the crewmembers and civilians that have died so far, a never-ending task that leaves her no time to see Akito.

Having made it to Mars, the Nadesico fends off an attack and locates an underground colony of survivors. But rather than being grateful to be rescued, the survivors have no intention of leaving their home, because they believe the Nadesico will be desroyed before it gets back to Earth! Can Yurika prove that the Nadesico is up to the task, or is the colonists' dire prediction all too accurate?

Whilst Yurika and Inez put together a ""Get to Know the Nadesico"" broadcast to explain the Nadesico's recent adventures on Mars, the crew's thoughts turn towards finding a way to repair their ship enough to leave Mars and head home. Meanwhile, Akito has issues of his own to work through when he learns that it was Admiral Fukube's fault the Jovian chulip destroyed his home on Mars.

The Nadesico returns to Earth via the tulip on Mars, only to find that 8 months have passed while they were inside the chulip, and that Nergal has built a second battleship. Meanwhile, on the battlefield, Akito discovers that his paralysing fear has returned, making him a vulnerable target for the Jovians...

Whilst Admiral Munetake sends the Nadesico to rescue a goodwill ambassador from a glacier, Megumi decides to use her free time to get closer to Akito in a virtual reality simulation of a high school fantasy. But can Akito commit to Megumi when his childhood memories of Yurika keep interfering?

Despite being ordered to investigate a giant chulip on a tropical island, the crew decide to first enjoy some swimsuit time at the beach. Meanwhile, having slipped away from the attentions of his admirers and their nightmarish attempts at cooking, Akito runs into a girl who seems to embody his idea of the perfect woman. Can reality ever match up to fantasy, or is Akito in for a big disappointment?

The Nadesico finds itself in trouble when they are taken down by a micro black hole from a new land-based Jovian cannon called the ""walking stick"". Now it is up to the Aestivalis pilots to reach the walking stick and destroy it before it recharges, but Akito fears that unless his colleagues can figure out the meaning of teamwork, the mission won't go well.

When the Nadesico's computer system malfunctions and starts attacking United Earth forces vessels, Admiral Munetake decides that the ship's memory banks should be wiped and reinstalled. Unwilling to see Omoikane (the ship's AI) and all its valuable data erased, Ruri enlists Akito's aid on a virtual reality mission to save Omoikane and restore its sanity.

It's Christmas on board the Nadesico, but behind the veneer of festivities, more serious events are moving forwards. With the Nadesico set to join the military, the crew face being being drafted into the UEAF- all except Akito, that is, who is set to be replaced by a trained pilot. Taking advantage of this opportunity, Erina asks Akito to help further her research into organic boson jumping (teleportation). But is being a pawn in one of Erina's games really worth the risks, or should Akito just forget it and spend a quiet holiday with Megumi?

In a reversal of perspective, the Gekigangar crew settle down to watch the latest adventures of the Nadesico. Unfortunately, with no time to put together new footage, the Nadesico crew instead present a clip show, including information on the ship, the crew, and all their adventures to date.

Whilst the Nadesico heads to the Moon to pick up Akito, Munetake suspects that the pilots of the Jovian robot they recovered from Earth may be hiding somewhere on the ship. Uribatake is ordered to track down the intruder, but will anybody on board be prepared for the consequences of discovering the true nature of the Jovians?

Whilst the Nadesico docks at the moon to await the launching of its sister ship the Shakuyaku, Megumi and Minato are taken aboard the Jovian starship, crewed by the ""Superior Male"" Gekigangar fanboys. But there are revelations for everyone as the crew learns the truth about the origin of the Jovians, not to mention the realisation that there were those who already knew the whole story, and chose to keep it quiet…

When Nergal finds out that Uribatake has been embezzling funds and spending a lot of time with Hikaru, Yurika drags Akito along on a special investigation to find out just exactly what the chief engineer has been getting up to. Meanwhile, when Munetake discovers that he may be demoted, he desperately searches for a way to get back into the military's good books.

It's revelation time for Ruri when she discovers that she is the biological daughter of the King and Queen of the neutral country Peaceland, who was lost after an in vitro fertilisation. With Akito as her knight, Princess Ruri heads off on a journey to fill in the missing details of her past.

Nergal decides that Nadesico crew needs to kept happy with a bright and beautiful new captain- and what better way to select one than with a talent contest? Believing the contest is just to raise morale, Yurika readily agrees, and all the crew gets excited about showing off. All, that is, except Ryoko, who wonders whether she has any other talents than fighting and killing.

Yurika must use all her tactical skills to save the ship from the Jovian's 'leap cannon'- a weapon capable of teleporting warheads right inside the Nadesico. Can Yurika prove that she's more than just a ditz by taking down this new threat?

The Nadesico has been tasked with defending the moon using its new phase transition cannon, but when something goes wrong with the Y Unit, the weapon becomes inoperable. With only an hour to fix it, the ship's pilots are sent down to traverse the now hazardous corridors leading down to the Y Unit and find out what has happened, a task made all the more difficult by the fact that their minds have become linked together into an illusory ""memory mahjongg"" game, whilst repressed portions of their personalities take control of their bodies...

The Jovians have sent a peace emissary over to the Nadesico- Yukina Shiratori, younger sister of Tsukumo. However, peace is the last thing on Yukina's mind- she plans to assassinate Minato, the 'savage Earth woman' who 'corrupted' her brother! And with the Nadesico about to arrive back on Earth, how will Nergal and the UEAF react to there being a Jovian aboard the ship?

Having left the ship, the Nadesico crew attempt to settle back into their old lives on Earth, despite the fact that Nergal is keeping a close eye on them. But the longer they stay on Earth, the more the crewmembers begin to realise how important it is to finish what they started on the Nadesico...

Truth, peace, and justice- these are the ideals that the Nadesico wants both warring sides to appreciate, and what could embody them better than the century-old Gekigangar anime? Whilst Tsukumo Shiratori arrives on board ot act as an ambassador, Yurika organises a shipwide ""Geki-Fest"", hoping that the themes of the show will help both Earthlings and Jovians understand how to achieve peace.

The ancient ruins on Mars and the control they offer over boson jumping have become the prize that everyone wants to claim- not least Akatsuki and Nergal. As the Jovians gear up for a final offensive, the Nadesico crew find themselves working with sister ship the Kakitsubata to make sure Nergal comes out on top.