Plot

When the Terran Confederation faces the possibility of humanity losing the war with the Kilrathi, Colonel Christopher Blair (Mark Hamill), who the Kilrathi have dubbed "The Heart of the Tiger", is summoned.

The war with the Kilrathi has lasted for generations, now the Terran Confederation faces the possibility of humanity losing the war, and Earth being over-run by the cat-like race of the Kilrathi. In a desperate attempt to win, the Terran Confederation prepares to destroy Kilrah; the Kilrathi home-world, and end the war. But only one man is qualified; Colonel Christopher Blair (Mark Hamill), who the Kilrathi have dubbed "The Heart of the Tiger".—John Betancourt <MXKM38B@prodigy.com>

The game opens to a cinematic sequence of two Kilrathi fighters landing in Kilrah's capital city. A group of humans have been captured and their fate is being decided by senior members of the Kilrathi government. The Kilrathi are a fearsome, marital race of formidable, tiger-like creatures and decide that the prisoners are not soldiers worthy of any respect and are disintegrated on the spot&mdash;with one exception. Col. Jeanette "Angel" Devereaux, (Yolanda Jilot) the hero's girlfriend from prequels, is regarded as a warrior on the contrary. She is promised what the Kilrathi consider a great honour, but the scene closes before we can witness it. But not before we are made aware that the hero, Col. Christopher Blair (Mark Hamill) is "The Heart of the Tiger".

Blair and Paladin (John Rhys-Davies) are standing at the edge of a water body as small air/spacecraft fly around them and the TCS Concordia (a carrier that Blair was assigned to in the last game) which has now crashed into that water body. Blair asks Paladin if anything new is known of Angel and Paladin denies all knowledge, but he appears to know more than he's letting on. Blair doesn't believe him anyway.

Aboard some space-borne construction, Admiral Tolwyn (Malcolm McDowell) (a frequent antagonist of Blair's) informs Blair that he has been assigned to the TCS Victory. Blair seems very reluctant to take this assignment, but Tolwyn is unmoved. The admiral then describes the progress of the war as favourable. Blair does not address that, but proceeds to direct the admiral's attention to a request he had previously made. Tolwyn is also dismissive of this request, indicating that it involved Angel, and is then dismissive of Blair's continued presence in his office.

Aboard a shuttle, Blair watches a news report about leaked information suggesting that the Confederation is preparing for the destruction of Earth by colonizing other planets, in stark contrast to the professed optimism of the brass.

Aboard the Victory, Blair is introduced to some of her crew, and reintroduced to some of his old friends. Capt. William Eisen (Jason Bernard) commands her. Col. Ralgha "Hobbes" nar Hhallas, (voiced by John Schuck) a Kilrathi defector, is also there to greet him. Unfortunately, Maniac (Tom Wilson) is also there to be obnoxious, egotistical, arrogant and bitter about Blair's improved popularity over his. New to the Wing Commander universe is Chief Technician Rachel Coriolis (Ginger Lynn), "Radio" Rollins (Courtney Gains) as are the pilots, Robin "Flint" Peters (Jennifer MacDonald), "Vagabond" (François Chau), and "Vaquero" (Julian Reyes).

Most of the missions are basically the same in Wing Commander III has they have been with every Wing Commander instalment: Blair flies patrol or strike missions aboard various fighters (some of which are bomber class) equipped with various types of projectile weapons, missiles, and countermeasures. There are variations, however. Sometimes he flies escort missions, in one mission Blair has to content with an unusual enemy cloaking torpedo known as a "skipper", and then there's the rescue mission. For every mission the player is allowed to select the equipment on board his craft, although, his selection of available craft is limited. In most cases he has a wingman. In between combat missions, we are treated to cinematic sequences of Blair socializing with the crew or depictions of other plot-related events. In a typical conversation that Blair has with someone, the player is given the option of choosing among two different lines of conversation, which usually have a bearing on the crew's morale. In general, these decisions effect the behaviour of all the non-player characters.

When Blair first meets Rollins, it is apparent that the kid is given to conspiracy theories. He is made to look somewhat paranoid and foolish for this, but in the end, he is vindicated for some of his suspicions. "Cobra" (B.J. Jefferson) is a former POW of the Kilrathi. Consequently, she has experienced the most unspeakable atrocities and is loathsome of the Kilrathi and makes no exceptions for Hobbes. Hobbes acquitted himself as being loyal to the Confederation in previous games, as a matter of principle, and is an old friend and wingman of Blair's. He had difficulty in overcoming Blair's prejudice in Wing Commander II and now faces the same problem with the unfamiliar Victory crew.

During a set of missions, Admiral Tolwyn comes on board and takes command. Tensions rise as the crew does not have as much confidence in Tolwyn as they do in Capt. Eisen. During a briefing, Tolwyn reveals the development of a weapon called the Behemoth. It is a space-borne vehicle, but essentially just an enormous directed energy weapon with engines and enough firepower to utterly destroy a planet. It is then revealed that production of this weapon was hurried because the war effort is very grim. In fact, Tolwyn now admits that the Kilrathi are on track to overrun Earth in six months! Unfortunately, a traitor is on board the Victory and the Kilrathi High Command are given schematics of the Behemoth. During the mission that was to see Kilrah destroyed, a weakness is exploited in the Behemoth and it is destroyed.

The traitor is revealed to be Hobbes. He kills Cobra as he makes his escape in a fighter. (During a deleted scene it is revealed that Hobbes did not know he was a sleeper agent. He was conditioned with a personality sympathetic to humans. When he was activated, this personality was replaced by his true personality.) Eventually, Blair goes one-on-one with Hobbes in a combat mission where Hobbes dies.

During a mission where Blair becomes entangled in combat with Prince Thrakhath (voiced by John Rhys-Davies) he learns what became of Angel. We then see it for ourselves: it would appear that the Kilrathi believe it is an honour to have your enemy rip your heart out of its rib cage and eat it, while you are alive and conscious. This is the gesture of respect they paid to the warrior Angel.

Blair is understandably devastated. When he confronts Paladin, his old friend reveals that he knew this all along. At the player's option, he can punch Paladin in the jaw for keeping this from Blair. In any case, Paladin reveals that Angel's death can have meaning.

Blair is assigned to a bombing mission that will single-handedly end the war. A Temblor bomb, so-named after the scientist who created it, is to be dropped on Kilrah. Angel's mission was to analyse the tectonic makeup of the Kilrathi homeworld. The data recovered from this revealed that it could be disrupted in such as away as to destroy the planet as surely as the Behemoth could have. The Temblor bomb was designed for this exact purpose.

The hero does just that and Kilrah is destroyed along with her emperor. Blair's ship, however, is also damaged in the blast. It is captured by a Kilrathi capital ship and the colonel is taken before its commander. He fully expects to die, but is as defiant as such a hero should be, but secure knowing that he has saved humanity. Seeing their cause is lost, the massive cat spares the human and informally announces to him that the Kilrathi surrender.

In the end, the relationship with either Rachel or Flint is brought to fruition, depending on decisions made during interactive sequences. Of course, if he pursues a relationship with neither, he is seen been shuttled to his next assignment alone.