A very vivid and horrifying nightmare plagues not only Hibiki, but also Dita, Meia, and Jura as well. While they struggle to figure out the meaning of this strange dream, a mysterious pod appears which the Harvest fleet seems to have a vested interest in. Deciding to capture the pod, the Nirvana launches its pilots to retrieve it - but when the events of the nightmare repeat themselves, Hibiki and the others must do whatever they can to make sure that their nightmare doesn't turn into a chilling reality. The contents of the pod, meanwhile, may prove to make things more interesting on the Nirvana than ever.

The message inside the pod that Misty was frozen in contain something that may be of use to the crew of the Nirvana, but the password proves to be a brick wall that BC can't seem to pass. Even worse is the fact that BC's attempts to crack the password shut the ship down, leaving it completely defenseless to an enemy attempt to tow the Nirvana away to be harvested. The Dreads outside have to stop the enemy, but they have to do it without Dita and Hibiki, who are stuck in a stopped elevator with Ezra, who has just began to go into labor!

The Nirvana arrives at yet another planet tampered with by the Harvest fleet, as its inhabitants are unable to survive the air and have all caught a disease that is fatal, with no cure. On a mission of mercy, Duero and the rest of the crew stop at the planet in order to ease people's suffering and help them, and Bart befriends a little girl named Shirley, also bedridden with the disease. However, yet another enemy attack threatens the crew's only attempt to create a clean environment for the inhabitant's babies to be born in, and a reluctant yet determined Bart must leave Shirley to fight for her life while he fights to defend the planet from attack.

The Nirvana comes upon another Mission, though the inhabitants are decidedly hostile and use a law of ""take what you want by force"" in order to survive. Hand to hand combat is the only way to prove the Nirvana crew's strength, and BC, as the highest ranking officer on the away team, chooses to fight in order to prove the Nirvana's good will. The enemy, however, isn't about to stop for a simple fight, and the Mission becomes infested by Harvest fleet units. With energy weapons useless against these new enemies, Barnette's antique gun selection using old fashioned ""bullets"" may be the only thing to keep the Mission from being harvested, although an old acquaintance may make an appearance as well...

Another Harvest fleet mother ship has come to attempt to attack the Nirvana, and the crew, this time, sets out confidently to destroy it using the same methods as before. However, a new form of enemy beats back the attack of the Dreads and Vandreads, and after Jura suffers serious injury, Gascogne is forced to pull rank and push for a retreat, towing an unwilling and furious Barnette from the battlefield. Jura's injury and condition cause Barnette and Hibiki to bristle and Gascogne's seemingly cold and calm attitude, and a heated argument ensues. Hibiki and Barnette find, however, the Gascogne knows much more about the pain of losing someone than anyone else, and that staying calm is the only way to win battles. And Gascogne is willing to teach everyone that lesson, at any cost...

The second attack on the Harvest mother ship has failed, although now Hibiki and the others have a ray of hope in the form of a way to penetrate the mother ship's defenses. Forming a plan around Parfait's limited ability to stop the machine-controlled Harvest fleet, Hibiki and the others launch one last, desperate attack on the mother ship, using Pyoro to upload a virus directly from the mother ship's core. Now the Vandreads must defend the little NAVI robot as he struggles to do his job - but the new enemy form is not far behind...

Things have once again lulled, and the crew now can turn to more important things - such as using cameras to observe the continuing soap opera between Misty, Dita, and Hibiki - a battle the Misty appears to be winning with her knowledge about men and women. A depressed Dita's feelings are hurt, and a guilty Hibiki is left wondering what to do to cheer her up again. Meanwhile, Jura becomes tired of all the beating around the bush and is determined to resolve the rift between Dita and Hibiki once an for all...

The Nirvana nears home, and only has to pass through an incredibly large electromagnetic storm in order to be in their home solar system. However, during yet another battle with the Harvest fleet inside the storm, Hibiki is lost, thrown to parts unknown. As the crew of the Nirvana frantically searches for Hibiki, Hibiki finds himself on a planet with people that have a unique take on destiny and the ""spirits"" that guide them. In order to clear his turbulent mind, Hibiki must now pass the ""trial of himself"" in order to leave - but all the doubts from before may come back to haunt him. Meanwhile, Duero makes an interesting discovery about Hibiki's heritage.

The Nirvana has finally reached its home solar system, but the Harvest fleet's remaining mother ships are not far behind. Despite this, the crew decides to hold a party to celebrate their coming home - that is, until they encounter their last obstacle to their home planets - a Tarak mobile mine field that threatens to destroy them all! With no desire to break through the field because it might slow down the Harvest fleet behind them, the crew of the Nirvana is left to guess the password to call off the system before it destroys them. Unfortunately, only senior officers of Tarak know the password, and time is quickly running out - until the password comes from a most unexpected source...

Having come through the minefield, the entire crew of the Nirvana is promptly captured by both Tarak and Mejale fleets. The men are to be forcefully ""re-educated"" for their desire to be with women, and the women are put on trial and imprisoned. With all seemingly lost, and the Harvest fleet on the way, the Nirvana and its crew are powerless to stop anything. But Hibiki, along with a few other key individuals, may be able to turn the tables and get the Nirvana back from its captors.

With the Nirvana back on track, all that is left now is to defend Tarak and Mejale from harvesting. But the Nirvana and the veteran pirate ship with it might not even be close to being able to fight off three or four motherships. It has come time to unite the two cultures in battle against the one, true enemy that threatens them all, but it may take Hibiki and his newfound knowledge about proving one's own existence to motivate them all to join the final battle against Earth's Harvest fleet.

Combined, the fleet of ships continues to destroy ship after ship of the harvest fleet. But the Main Mothership is another story, and even the combined Super Vandread is no match for it. With Hibiki captured by the leader of the Earth Harvest fleet, and the Dreads similarly restrained, all looks lost. But as the leader of the Harvest may find, it will take a lot more than a few wounds and losses to keep Hibiki and his friends down. With one last strike, Earth intends to end all resistance...and it may take the combined might of everyone with the will to live to stop the Harvest fleet once and for all.