After an attack by two unidentifiable spacecraft, the computers aboard Liberator turn on Blake and his crew through the intervention of the ship's original owners, who are controlled by a massive computer called The System.
Blake tries to buy the services of the Terra Nostra organized crime syndicate in his struggle against the Federation. When his first effort fails, he decides to go after their biggest source of profit to gain leverage. That source is an illicit narcotic called shadow.
After a researcher named Coser kills his superiors at the Federation's weapons development base, he escapes to a deserted planet with a new secret weapon called IMIPAK. Soon, both the Liberator's crew and Servalan are searching for him.
The Liberator arrives at the planet Horizon when the Liberator follows a Federation freighter. Blake and Jenna teleport to the surface, only to be taken captive by Federation guards. Shortly after Cally, Gan and Vila are also taken captive and forced to work in the mines. Avon decides to leave the crew on Horizon and take control of the Liberator, but instead, teleports to the surface to rescue them.
The Liberator returns to Earth where Blake plans to attack the Federation Central Control computer complex. But Blake's contact, Kasabi and her daughter Veron have been taken prisoner by Servalan and Travis and Blake and Gan teleport to the surface to find Veron and outrun the security devices on the outer perimeter of the Central Control computer complex.
Holding himself responsible for Gan's death, after Gan was killed by Travis at the Central Control computer complex on Earth. Blake decides to desert the crew and teleports to the surface of a volcanic planet, where he finds he is not alone. Travis is standing trial at Federation HQ for the massacre of innocent people. Travis's trial is Servalan's cover up of the incident at the Central Control computer complex.
Avon and Vila teleport to a Federation installation on the planet Fosforon to meet an old friend of Avon's in hopes of stealing a key component of the Federation's cipher coding system. Meanwhile, Blake becomes involved with the base's investigation into the appearance of a spacecraft listed as missing 700 years ago that has suddenly appeared near Fosforon.
The Liberator crew learns Travis is on the planet Exbar where Travis has taken Blake's cousin Inga hostage demanding Blake comes to Exbar to meet with him or he will kill her, where he wants to join the Liberator crew, now he is a Federation outlaw. Travis sets a trap for Blake, Avon and Vila. Servalan also arrives on Exbar.
The Liberator heads to the Federation controlled planet Albian, where Blake and the crew are in search of Federation officer Space Major Provine whom they believe can lead them to the location of Central Control. Only to learn The Federation has buried a radioactive bomb on the planet which wipe out all life on Albian. As Blake and the crew helps a band of rebels find the bomb. Avon meets up with enemy Del Grant, brother of Avon's former lover Anna and tries to disarm the bomb and puts aside his differences with Grant.
As The Liberator heads to Del 10 Blake receives a subliminal signal to reroute to an asteroid where he finds Shivan, a resistance leader and Governor Le Grand who need The Liberator to transport them to Atlay where they are to hold a summit to denounce the Federation. But is all what it seems?
The Liberator travels to the gambling paradise of Freedom City, where Blake is in search of a cybernetics surgeon known as Docholli who knows the location of Star One, the Federation power base. However, Servalan has implanted a bomb in Travis' robotic arm, which will kill both Blake and Travis, and Travis requires Docholli's help to remove the bomb.
The Liberator sets a course for the planet Goth, where Blake, Jenna and Vila teleports to the surface and goes in search of a amulet that belongs to the royal family containing the location of Star One. But Travis too has arrived on Goth and is also after the amulet and Blake agrees to rescue Rod, brother of the planet's ruler Gola.
Blake leads the apprehensive crew of the Liberator out into intergalactic space to find and destroy Star One and cripple the Federation. What none of them realize is that Star One is already showing signs of sabotage. But since nobody but Blake's crew know the location of Star One, who could be causing it, and why?