The Nadesico heads out to the Satsuki Midori space colony to pick up some new zero-G Aestivalis frames and pilots. After an explosion rocks the colony and disables it, their mission becomes one of rescue and retrieval.

The Nadesico heads to 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 defy Earth and force their way through?

With the Jovian fleet closing in, it's up to the Nadesico to keep the ancient Martian ruins out of enemy hands. Unfortunately, it's beginning to look like the only way they're going to be able to do that is to destroy them!

As the Jovians gear up for a final offensive, the Nadesico crew find themselves working alongside their sister ship, the Kakitsubata, to maintain control over Mars.

When Tsukumo arrives on board to act as an ambassador, Yurika organizes a ship wide "Geki-Fest". She hopes that the themes of the show will serve as a guide for both the Earthlings and Jovians on how to achieve peace.

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

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

The Nadesico's new mission is 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 repair it, the ship's pilots must discover what happened, a task made all the more difficult because their minds are currently linked in an illusory "memory mahjongg" game.

The Jovian's have a new weapon - the "leap cannon". Capable of teleporting warheads inside of ships, it's potential is devastating. Can Yurika save the Nadesico and prove that she's more than just a ditz?

Uneasy about the idea of a powerful battleship being 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?

Nergal decides that to keep the Nadesico crew happy, they're going to give them a new captain! And what better way to pick one than to hold a talent contest? Yurika agrees, and everyone gets excited about the chance to show off. Everyone that is, except Ryoko, who wonders whether she has any other talents besides fighting and killing.

Ruri discovers that she's the biological daughter of the King and Queen of a kingdom called Peaceland. With Akito acting as her "knight", Ruri sets off to Peaceland in the hope of filling in the gaps in her memory.

Nergal discovers 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 up to. Meanwhile, when Admiral Munetake discovers that he may be demoted, he'll do anything to get back into the military’s good graces.

The revelation of the true nature of the Jovians has shaken some of the Nergal employees. Could spies in their midst already know about their secret plans? Meanwhile, Tsukumo takes Megumi and Minato to a Jovian starship. Surprises abound for the entire Nadesico crew as they learn the truth about their enemy.

Whilst Akito is trapped on the moon, back on the Nadesico Admiral Munetake suspects that the pilot of the Jovian robot they recovered may be hiding somewhere on the ship. But will anybody on board be prepared for the consequences of discovering the true nature of the Jovians?

In a reversal of perspective, the Gekigangar crew settle down to watch the latest adventures of their favorite show: Martian Successor 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.

Christmas may be near at hand, but it's not going to be a happy holiday for the crew of the Nadesico. The UEAF doesn't want such a powerful warship under the command of civilians and is giving the crew a choice: join the military or get off the ship. Taking advantage of the opportunity, Erina offers Akito a job assisting in her organic boson jumping research. But is being a her pawn really worth the risk, or should he just forget about the offer and spend a quiet holiday with Megumi?

When the Nadesico’s defense system malfunctions and starts attacking United Earth forces vessels, Admiral Munetake decides that the ship’s memory banks should be completely wiped. Unwilling to see Omoikane erased, Ruri enlists Akito’s aid on a VR mission to save Omoikane.

The Nadesico finds itself in trouble when they are given a mission to take out a new Jovian weapon called a "Walking Stick". After the weapon's initial offensive critically damages the Nadesico's systems, it's up to the Aestivalis pilots to reach the deadly weapon and destroy it before it can recharge for a second barrage. But if the pilots can figure out the true meaning of teamwork soon, it might spell the end for the Nadesico.

Admiral Munetake announces that the crew's next mission is to the Tenician Island to investigate anew type of chulip. But the tropical island with its shining beaches may prove more of a distraction for the crew. Meanwhile, Akito runs into a girl who seems to embody his idea of the perfect woman. Can reality ever match up to his fantasies, or is Akito in for a big disappointment?