Meia is in trouble! Seriously injured in a battle, and having some 'personal issues' as a result, she is facing quite a struggle for her life. The other pilots do not handle the idea that they may have to replace Meia well, and Jura is unable to command the Dreads in her place. Duero, Parfait, and Paiway struggle to save Meia's life as Meia has flashbacks to her turbulent and troubled past. The latest enemy attack may hinder their ability to bring her back from the brink of death, however, and it is left to Hibiki, of all people, to come up with a plan that just might save them all.

The crew of the Nirvana come across a planet that is almost completely covered in water. There is one island on the planet, but before they have time to investigate they must face cubed shaped opponents. Jura is as determined as ever to unite with Hibiki, and this is the perfect opportunity for her to do so - although the result may not be what she was necessarily expecting. As Hibiki and Jura crash onto the surface of the planet, the Captain and B.C. go down to investigate, and meet the locals, who seem to be willing to be harvested by the Harvest fleet. Meia and Dita try to desperately hold off the new Harvest fleet ship that is approaching the planet, but it may take Hibiki to motivate an extremely depressed Jura to fight in the new Vandread in order to save everyone.

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...

Every single year, Meia dreads one day - her birthday, when the crew attempts to surprise her with a party. Meia has managed to run away every single year, but this year, Hibiki is here, and he decides to help out the women. Shaking up the plans the women use every year, Hibiki's scouting cuts off every possible escape route for Meia. But when Meia decides to go to Magno with her complaints, Hibiki and the others have to find the perfect thing to keep Meia busy until they can plan the party - even if it happens to be a certain newborn baby.

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.

Summary of Vandread the Second Stage plus several extra scenes.