James 'Paladin' Taggart (John Rhys-Davies), a senior governor of the Assembly, declares that the Assembly must cast a vote on whether or not to declare war on the Border Worlds, with Admiral Geoffrey Tolwyn (Malcolm McDowell) assigned to a fact-finding mission which will essentially decide the issue. Colonel Christopher 'Maverick' Blair (Mark Hamill), retired, is trying to make out a living on a desert world as a farmer, when he is recalled to active military service by Tolwyn. Within five minutes of Blair taking the cockpit, the station he's heading to is attacked by an Avenger-class fighter claiming Border Worlds allegiance. Border World claims that similar strikes that have occurred on their ships are ignored. Tolwyn assigns Blair to the TCS Lexington with the task of unraveling these tensions and getting to the bottom of the story. Blair is reunited with Lexington's new captain, William Eisen (Jason Bernard), Major Todd 'Maniac' Marshall (Tom Wilson), and Lieutenant Winston 'Vagabond' Chang (François Chau). Blair also meets Lieutenant Troy 'Catscratch' Carter (Mark Dacascos), a Kilrath-o-phobe who joined the military a couple of years too late.
Blair can find no concrete evidence, and no one can positively identify the harassing ships. Tolwyn transfers a new officer to the Lex, Captain Hugh Paulsen (John Spencer), who replaces Eisen in command. After flying sorties under Paulsen's command, Blair either heads to the officer's lounge with Maniac or ventures down to the flight deck without proper authorization. If Blair heads to the lounge, Maniac abruptly leaves him at the lounge bar remembering "something he has to do." If Blair sneaks onto the flight deck, he witnesses Seether (Robert Rusler) arriving in a shuttle and meeting Paulsen. Soon after, Paulsen calls Blair and Chang in for a surprise mission briefing: Eisen has defected to the Border Worlds and is fleeing in a shuttle, with Maniac piloting. Once in space, Vagabond announces that he is going to follow Eisen over. If Blair does not defect, he returns to the Lexington to meet a new cadre of pilots brought in by Paulsen. Blair flies with them for several missions before being confronted with a Border Worlds attack, led by Maniac, who gives Blair another chance to come over.
If Blair defects with Vagabond, he arrives with Eisen, Maniac, Vagabond and Catscratch at the BWS Intrepid, an old Durango-class carrier that has recently suffered damage from a Confed attack. Much of the senior staff has been killed, including Eisen's contact (and old friend) Captain Dominguez. The two officers currently sharing the command, Colonels Jacob 'Hawk' Manley (Chris Mulkey) and Tamara 'Panther' Farnsworth (Elizabeth Barondes), assign Blair as Wing Commander for the flight group, and Eisen becomes her captain. Other Intrepid natives include Chief Technician Robert "Pliers" Sykes (Richard Riehle), Colonel John 'Gash' Dekker (Jeremy Roberts), head of the ship's contingent of Marines; and communications technician Lieutenant Velina Sosa (Holly Gagnier), whom Catscratch quickly takes a shine to. Eisen confides that he's been in touch with connections back on Earth, and it seems that the nascent Confed-Border Worlds war is being instigated by elements within Confed. He defected so that he could hunt for proof of this. Blair and Maniac succeed in downing the Lexington, though Paulsen escapes in a shuttle with Seether. Seether kills Paulsen for his failure.
Pliers comes up with a jerry-rigged cloaking device and a "Manned Insertion Pod"—a coffin-sized torpedo that can be used to land ground troops. Blair takes them in against a communications station in the Orestes System, where Sosa and Vagabond collect valuable data on the conspiracy. Vagabond is killed in the gunfight.
Blair picks up a distress signal from the Kilrathi Melek and rescues the convoy. Melek brings flight recorder data of the sleek black ships using their incineration weapon against a Kilrathi transport. One of the ships pulls a move that Blair saw in the attack on the space port, using the ship's afterburners to supercharge and detonate an explosive mine which pushes the ship away at a faster rate. Hawk tells them that when he signed on with Confed, there was a rookie pilot on his ship, call sign 'Seether', who could pull off the maneuver. He also informs them that there was some talk of a 'G.E.' program, but that he never found out what it was, and Seether was transferred from the flight roster to Confed Intelligence Operations. Eisen leaves the Intrepid, intent on returning to Earth and delivering the information to friends in high places; he leaves Blair as acting captain reporting to Border Worlds Rear Admiral Eugene Wilford. Finally, the Intrepid catches wind of a secret Confed freighter sneaking through the area. Blair subdues it so that Dekker and his boys can capture it. Pliers, clambering aboard in the aftermath, discovers a squadron of sleek black fighters and a single example of their incendiary weapon, called "Dragons" and "Flash-Paks" respectively.
The Telamon system is under biological attack. The vast majority of the colony, particularly Planet FT957, has died. Few survive the attacks, hale and untouched, evidently due to an innate immunity. The survivors at the colony recount that visiting Dragons dropped canisters containing a biological weapon. Blair traces the attacking Dragons to the Axius System, which he infiltrates. There he discovers a secret starbase, guarded by the TCS Vesuvius, and manned by thousands of black-clad soldiers, including Seether, collectively known as the Black Lance. Blair learns that their leader is Admiral Geoffrey Tolwyn, who is instigating a war between the Border Worlds and Confed, with the goal being constant war-driven evolution of tactics and technology, to prepare the Confederation to meet the next hostile alien race. The Gen-Select Bioweapon, recently tested at Telamon, is the next obvious step in the plan: a virus that kills off all but the most genetically superior. Blair is spied by Seether and forced to fight his way out.
