Most of the game takes place around a giant space cruiser named Dante.
The Planet Hornet is being threatened by a powerful space cruiser named Dante that is approaching them, intent on destroying the planet with a powerful weapon known as the Fermion Cannon. With a military shortage on the planet, it's up to a small group of released criminals to stop the ship, and save Hornet. However, not all is as it appears, as there are secrets hidden within the ship, secrets that point to members of the team hired to stop it.
- Jutah Fate: The main character, a bio-engineered soldier. He was sentenced to life in prison for warcrimes he committed on a mission, causing him to withdraw into his own mind. He was released from prison and placed on the team to destroy the Dante.
- Annri Ohara: A military officer in charge of the group. She is a computer specialist, and tends to crack under pressure. Eventually develops feelings for Jutah, and helps him come out of his mental shell.
- Benoit Manderubro: A political revolutionary, he sees politics as a giant game and likes to manipulate the pieces to see how they react. His skill at fighting is said to exceed even Jutah's.
- Micino Tifone: A professional and beautiful spy. Her agility is second to none and it is said there are no secrets outside of her grasp.
- John Loss: A fighter for a small tribe of people from a small planet. He joined the group in exchange for getting rights for his people. Though usually quiet he goes into a beserker rage when in combat.
- Tim Palmer: An ace pilot assigned to the group. He is said to be capable of piloting any vehicle, even if he hasn't been trained in its use.
References in .hack
- Each of the main characters of Silent Bomber reappear as NPCs in the .hack//Games. They carry rare items that players can trade them for in exchange for elemental items, or Golden/Silver Axes.
- Silent Bomber, a rare Wavemaster weapon, has a skill named "Stuck?" which summons a Nosferatu version of Jutah.
- In the .hack//Games, an advertisement for Silent Bomber is shown on the top of the screen when reading the news. According to .hack//analysis, this is the second of the two games created by the CyberConnect Corporation before The World.
- In the .hack//G.U. Games, there is an Arena team named "Silent Butcher".