The war between the alien Kilrathi Empire and the
Terran Confederation has been over for several years. Confed is attempting to stabilize its economy and social structure. The Kilrathi survivors, now led by
Melek nar Kiranka, retainer to the late Prince Thrakhath, are having greater problems than they had during the war, since their racial and societal makeup revolves around hunting and killing. Tension between the Confederation and the Union of Border Worlds has deepened, most recently with an attack on an unarmed medical transport. This transport is destroyed by a wing of mysterious fighters equipped with a new anti-ship weapon that incinerates the target's contents, leaving only a burning shell behind.
James 'Paladin' Taggart, 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 assigned to a fact-finding mission which will essentially decide the issue.
Colonel Christopher 'Maverick' Blair, 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 Worlds 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, Major Todd 'Maniac' Marshall, and Lieutenant Winston 'Vagabond' Chang. Blair also meets Lieutenant Troy 'Catscratch' Carter, a Kilrathiphobe 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, 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 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 and Tamara 'Panther' Farnsworth, assign Blair as Wing Commander for the flight group, and Eisen becomes her captain. Other
Intrepid natives include Chief Technician
Robert "Pliers" Sykes, Colonel
John 'Gash' Dekker, head of the ship's contingent of Marines; and communications technician Lieutenant Velina Sosa, 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. The
Intrepid, pursued by the
Vesuvius and Tolwyn's Black Lance pilots, makes a run toward Earth, intending to stop Tolwyn from addressing Congress. Though helped by the intervention of the TCS
Mount St. Helens, sister ship to the
Vesuvius, and its new captain, Eisen, the
Intrepid is unsuccessful in stopping Tolwyn. Blair duels Seether one-on-one above Earth and then lands at the Congressional Building. Tolwyn delivers his report on the Border Worlds and Blair slips in. If Blair makes a silent entrance, Tolwyn alerts the chamber guards to arrest Blair and he is not given a chance to speak, instead being executed. If Blair instead chooses to make a dramatic entrance, Paladin gives him the chance to speak before the Assembly. Blair baits Tolwyn into revealing his true agenda and admitting his crimes. If the player scores enough points against Tolwyn, the Senate votes against war. Tolwyn is then indicted and convicted for his actions; lacking an appeal, he hangs himself in his jail cell, rather than be executed. Blair will either regain his rank as Colonel and be seen helping Panther train new pilots at the Academy or using Black Lance assets to crush rebellions with Hawk at his side as the new Admiral, depending on the general tone of his choices throughout the game. If the player makes the wrong choices facing Tolwyn, Blair is convicted of treason and executed as the war begins. This also happens if at any time Blair is captured by Confederation forces after his defection. If Blair fails enough missions before his defection, he is simply sent back to his farm. ==Cast==