Hibiki starts as a member of a Tarak fleet, being a Vanguard Pilot rather than stealing one. He is the only male to board the Nirvana. He is also slightly less impulsive, and admits his feelings for Dita more openly.
Dita is less childish in the manga, and addresses Hibiki by name, rather than “Mr. Alien”.
Nearly half of the major cast does not appear, including Duelo, Pyoro, Magno, Paiway, Ezra, Gascogne, Misty, Rabat, and Butan. However, Bart appears in the first chapter, but not as a crew member of Nirvana.
Human beings from other planets don’t appear. The name Lord Grandpa and Grandma are not mentioned as the ruler of Taraak and Mejere respectively.
Hibiki’s Vanguard does not change from the Paxis, and there is only one Vandread and it is the form Hibiki and Dita share. Its fusion is also made permanent. An evil counterpart to the Vandread exists, called the Vandora.
Meia is captain of the Nirvana.
Jura is the fourth bridge operator rather than a Dread pilot.
Barnette, rather than lay her interests in Jura, sets her eyes on Hibiki instead.
B.C. is a female and is the main antagonist in the first manga. It is also revealed that she was in love with a man, meaning she did not come from Taraak, Mejere, or Earth.
In the anime, the enemy is called “The Harvest”, but in the manga, the enemy is called “Terran” which means invader. “Terran” can also be a reference to Terra the Latin name for Earth meaning a citizen of Earth. Since the enemy originated from the Earth this meaning is likely.
2 characters exist exclusive for the manga.
Tenhou Farland, a green-haired, 12 year old girl, with a unique ability to interact with machines and finds a surrogate brother in Hibiki.
Asra Mutie, the blue-haired pilot of the Vandora. She helps the Nirvana crew, only to know who they are. She initially plays a similar role of Misty from the anime, interacting with Hibiki and being more experienced in the relations between men and women, which causes jealously to Dita. When the Vandora takes control of Asra, Hibiki, Dita, and Tenhou save her, and Asra officially joins the crew.