Released in 1991, Wing Commander II retains much of the first game's core conventions: an interstellar war between the Terran Confederation and the felinoid warrior race called the Kilrathi, multiple allies as wingmen, and a wide variety of ships on both sides of the war. However, WC2 places a greater emphasis on storytelling, providing various sprite-animated cutscenes and some of the industry's first examples of voice acting. The storyline is also somewhat less open-ended: the game's campaign tree is much more structured and the player character can no longer be promoted or awarded medals. Wingmen can no longer be killed during normal gameplay; when their fighters are damaged beyond repair, they eject (though some die in scripted sequences). Finally, because the story is a direct sequel to WC1, many Kilrathi ships have names similar to the WC1 ships they replace (for instance, the "Sartha" replaces the "Salthi", and the Confederation uses an upgraded version of the Rapier medium fighter).
Expansion packs Special Operations 1 and 2, were released in 1991 and 1992, respectively, and a stand-alone spin-off, Wing Commander Academy, in 1993. Origin also released a Speech Accessory Pack, which upgraded WC2 with pre-recorded voice acting.
Cut to 2665, ten years later. Blair, flying a patrol, is startled to engage Kilrathi fightercraft in the area. Not long after, Admiral Tolwyn's flagship, the TCS Concordia, shows up on sensors, under heavy attack by a Kilrathi cruiser and her fighters. Blair and his wingman Captain Elizabeth "Shadow" Norwood together save the ship, and he is briefly reunited with some of his friends from the Claw—Colonel Jeannette Devereaux, Lieutenant Colonel Mariko Tanaka, the Kilrathi defector Colonel Ralgha nar Hhallas, Captain Etienne Montclair, and Major Zach Colson—and used to assist in the attack on the Kilrathi cruiser, before being packaged back to Caernarvon. Colonel Devereaux requested a transfer for Blair to the Concordia but on the flight back, Blair states to Shadow that he probably won't get reassigned due to his past with Admiral Tolwyn. But Blair and Shadow have barely returned when the Concordia is attacked again, and an explosion on the flight deck has crippled her ability to launch fighters. In the ensuing battle, Shadow is killed, Blair triumphs, and Tolwyn, ever-mindful of the need for good pilots, takes The Coward of K'Tithrak Mang onto his flagship.
Blair's time there is not particularly easy. At least one pilot, Captain Dirk "Stingray" Wright, believes the slander spread about the Claw's destruction, and he and Blair's stauncher supporters (Tanaka, nar Hhallas, Devereaux) are frequently at odds. The flight deck explosion, a bizarre murder, and radio transmission records suggests that there is a traitor aboard the Concordia. Tolwyn frequently credits Blair's successes to his wingmen (particularly nar Hhallas). And though Maverick encounters Kilrathi Strakha stealth fighters several times, his black box always manages to malfunction or be destroyed. His repeated claims regarding the invisible ships frustrate Devereaux, who despite her belief that he didn't have anything to do with the destruction of the Tiger's Claw does not believe his statements about the cloaked ships.
Not long into the campaign, Blair's oldest friend Mariko "Spirit" Tanaka approaches him with terrible news: the Kilrathi have her fiance Phillip. He was captured some ten years earlier when the Tiger's Claw defended the Firekka system from Kilrathi attack, and the Kilrathi are demanding her betrayal in exchange for his release. Even worse, Phillip is being held on the captured Heaven's Gate starbase, which Concordia has orders to destroy. In the end, Blair and Tanaka are assigned to the strike, but sabotage cripples Spirit's plane. With no recourse, she rams the station, destroying it, her fiance and herself in one herculean explosion. The news is not all bad, though: shared grief over their friend draws Blair and Jeannette "Angel" Devereaux into a budding romance.
Despite tragedy and setback, the tide begins to turn. Maverick and Angel fly a critical mission in which they trace a Kilrathi destroyer back to the K'Tithrak Mang, placing its location for the first time in the history of the Enigma Campaign. Blair is finally able to clear his name when he and Zach "Jazz" Colson engage Strakha stealth fighters and return, flight recorders intact, to tell the tale. Following an altercation with Angel when he reveals classified information he should not know, Jazz reveals that he, in fact, is the traitor who has been responsible for the message leaks, sabotages and murders, Blair is able to apprehend him. And, finally taking matters into his own hands, Blair flies a single-handed strike against the K'tithrak Mang, destroying it and defeating Imperial Crown Prince Thrakhath nar Kiranka in combat. If the campaign has not gone so well, Concordia jumps back to Gwynedd and Blair destroys a Kilrathi invasion fleet preventing a disastrous strike against Terra.
The hostile fighters are from the TCS Gettysburg, a Waterloo-class cruiser. She was stationed in the N'Tanya system, where a Kilrathi colony has been undergoing a rebellion against the Empire. Loyalist Kilrathi citizens were allowed to leave N'Tanya peacefully, but the Gettysburg's skipper, Commander Cain, ordered his pilots to open fire on their transports. The entire flight group, led by Wing Commander Col. Ransom, Lt. Col. Poelma, and Lt. Jason Bondarevsky, mutinied against the order to kill innocent civilians, and Cain was dispatched back to Confed HQ. Unfortunately, the mutineers soon parted ways: Ransom wanted to live as a pirate, while Poelma and Bondarevsky were all for returning to Confed. It was Ransom's group captured the Rigel depot; Poelma and Bondarevsky, in the meanwhile, have been promised pardons by Confed C-in-C. Blair is assigned to bring them back to the Concordia and destroy the Rigel depot. In doing so, he gets a chance to try out the Fleet's newest torpedo bomber, the YA-18A Crossbow, which the Gettysburg was field-testing. (The returning Gettysburg crew was acquitted, and Bondarevsky in fact promoted and decorated for his integrity.)
Taggart arrives aboard the Bonnie Heather and retrieves Blair and nar Hhallas, as well as Major Edmond, the Concordia's communications officer, for their Special Operations duties, which will take place on Olympus Station in the Ghorah Khar system. Like N'Tanya, Ghorah Khar is in rebellion, and Taggart's Special Operations involve helping these rebels succeed, in the form of contributions of leadership, pilots and war materiel. Blair also helps intercept a Loyalist dead drop, replacing the invasion plans contained within with Confed-developed plans that will lead the Kilrathi fleet into an ambush. Unfortunately, the Kilrathi arrive in far more force than anticipated, and Maverick and Hobbes fly several strikes against these attack groups.
At this point comes an unexpected complication: Taggart is ambushed at a jump point and the Heather crippled. All seems lost when another flight of Kilrathi ships jumps in... But they start shooting the first flight! Blair and Hobbes arrives, drive them off, and rescue an ejected Kilrathi pilot to see if they can get some answers. This ejected pilot turns out to be none other than Crown Prince Thrakhath nar Kiranka: the second flight, he explains, was an assassination attempt led by Khasra, a cousin of Thrakhath, in a bid for the throne of Kilrah. Though Thrakhath is imprisoned in the brig, a power failure allows him to escape; he grabs Hobbes's Crossbow and sorties out to avenge himself upon Khasra. Blair, attempting to retrieve him, is forced to help out, and the war's two best pilots together make short work of the Kilrathi rebels. Thrakhath, though, escapes.
The remaining Kilrathi fleet attempts to destroy Olympus Station once and for all; Olympus's flight group is already seriously thinned, and their communications have been jammed. Blair, leading the defense, knows his chances are grim... Until a group of pilots from the Gettysburg, sent along by a concerned Admiral Tolwyn, saves the day. With Ghorah Khar securely in Confederation hands, the N'Tanya, K'arakh and Shariha colonies manage to successfully rebel against the Empire. Unfortunately, Thrakhath, with tons of military intelligence in his head, takes advantage of the fact that the Enigma Sector fleets are distracted with Ghorah Khar and captures Deneb Sector Command in less than six hours.
The Mandarins begin transmitting propaganda movies, specifically the hijacking of several Terran freighters. The raids are quite clearly led by Zach Colson. The crews of the freighters are eventually traded for several Mandarin prisoners. Even worse, Thrakhath's ambitions are realized when a Mandarin traitor sets off a bomb on the Concordia's flight deck and steals a Morningstar. The traitor, Maria Grimaldi, heads for Ayer's Rock; clever deployment of Kilrathi patrols prevent Maverick and Maniac from following her.
Deciding that it's time for some cover agents of their own, Paladin takes over the Gamal Gan. He renames it the Grimalkin and transfers Maverick and Maniac back to Special Ops. Hiding two Morningstars aboard the Grimalkin, the three infiltrate the Ayer system. The Morningstar's torpedoes are supplemented by a new weapon: the Mace tactical nuclear missile. Though unguided, it can be detonated manually by the launching pilot, and does splash damage to whatever's in range. Minx makes it to an escape pod, but escape pods are not enough to prevent radiation poisoning. But Jazz stole her Morningstar, giving Maverick the opportunity to shoot him down before returning to the Concordia. Finally, in a humorous scene, Maniac's Morningstar, which broke down just after launch for the mission against Jazz, is seen drifting and deserted in space—evidently neither Blair nor Paladin cared to rescue him. (Maniac returns, hale and hearty, in the next game in the series, Wing Commander III: Heart of the Tiger.) Unfortunately, Thrakhath once again turns defeat into victory, by savaging the 6th Battle Fleet; the Confederation is forced to retreat, once again, from the Enigma sector.