Act I
Crane operator Abner Doolittle (Lewis Arquette) dredges up an old Mega War II biplane during construction of the new Megakat Marina. A veteran of the war, he recognizes it as belonging to "the most evil pilot who ever lived," an enemy ace known as the Red Lynx. Meanwhile, Chance and Jake are exercising. They catch Doolittle being interviewed on Kat's Eye News about the plane. Doolittle recounts how he witnessed the final battle between the Red Lynx and his arch-enemy, the heroic Blue Manx, Mayor Manx's great grandfather. Chance is a Mega War II aviation nut and has a great admiration for the Red Lynx's abilities, even if he was "on the wrong side."
Meanwhile, the biplane is taken to the Megakat City Museum of History. Curator Dr. Abby Sinian (from "The Pastmaster Always Rings Twice") discusses with security guard Charlie (Jim Cummings) how well-preserved the plane is despite how long it was submerged in the ocean. Sinian leaves and Charlie locks up. A shaft of moonlight shines down through the skylight and into the cockpit, causing the skeletal apparition of the Red Lynx (Mark Hamill) to manifest in the pilot's seat. He starts the engine and flies out, smashing through the skylight. He vows revenge against the Manx family, using his plane's antique machine guns to shoot at a billboard for Mayor Manx's reelection campaign.
At City Hall, Callie is in Manx's office writing a speech for him. As part of his campaign, the Mayor has commissioned a high-tech fighter jet named the Blue Manx after his grandfather, which it is hoped will give the Enforcers an edge over the SWAT Kats. The Red Lynx attacks the building, shooting through the window. Callie survives by hiding under the desk and the Red Lynx relents when he realizes Mayor Manx isn't in the office. He flies off in search of the Mayor with some Enforcer choppers in hot pursuit. He shoots down two of them and tricks a third into crashing into a skyscraper. Callie calls the SWAT Kats.
At the golf course, Manx is enjoying the solitude when suddenly the Red Lynx swoops in and begins shooting at him. He tries to flee in his golf cart, but the evil pilot disables it with gunfire, forcing the terrified Mayor to get out and run on foot. He falls into a sand trap and prepares to die as the Red Lynx takes aim at him, laughing insanely.
Act II
The SWAT Kats arrive in the Turbokat and pull Manx out of harm's way and up into the safety of the jet using the Sky Claw (the clawed mechanism on the end of a cable previously used to rescue Morbulus in The Giant Bacteria), then battle against his attacker. T-Bone initially mistakes their opponent for a Red Lynx imitator, but soon realizes it really is the vengeful ghost of the actual deceased Mega War II pilot. Quickly realizing that his antique plane is no match for the Turbokat, the Red Lynx flees, but vows that it isn't over.
Back at City Hall, Manx meets with Callie, the SWAT Kats and Commander Feral in his bullet-riddled office. The window is still broken. Manx is initially intent upon calling his reelection campaign quits and hiding out in his office, but Callie and the SWAT Kats persuade him that he needs to live up to the legacy of his heroic great grandfather and be brave, with Feral insisting that the Enforcers can handle "some old Mega War II pilot," dismissing the resurrected Red Lynx as no threat. They push Manx to attend the dedication ceremony for the new fighter jet, but he only agrees to go if the SWAT Kats will be there to protect him.
Callie goes to the museum and speaks to Dr. Sinian, who is unsure how the Red Lynx came back to life. The best she can figure is that his ghost is the manifestation of his deathless rage against his killer, and she promises to find a means of defeating him.
Later, Callie and Commander Feral attend the unveiling of the Blue Manx jet with the Mayor on the deck of an aircraft carrier. Manx gives a speech and then prepares to break a milk bottle over the nose of the jet when the Red Lynx reappears and strafes the carrier. Feral tries to call for reinforcements, but Manx knocks him into the ocean in a panic. The SWAT Kats arrived as promised and once more engaged their undead foe. Feral manages to climb back aboard the ship. Razor launches a missile at the Red Lynx, who dodges, and the missile hits and blows up a parked Jeep. The explosion sends Feral flying back overboard into the sea, but he survives. Finally, the SWAT Kats are able to use Slicer Missiles to cut the wings off of their enemy's biplane, and it crashes into the ocean and sinks. Composing himself, Manx finishes his speech and breaks the milk bottle over the Blue Manx's nose.
Later, Feral leaves two commandos (both voiced by Charlie Adler) to guard the Blue Manx aboard the docked aircraft carrier, but the Red Lynx's ghost sneaks aboard and takes over the experimental jet. The commandos attempt to stop him, but get blasted by the backwash of the jet's engines as it takes off.
Act III
Back at City Hall, Manx is selling hotdogs to schmooze with potential voters as Callie oversees the repairs to his office windows. Dr. Sinian calls with news that she's found out how to kill the Red Lynx for good. Callie initially dismisses her, thinking that the SWAT Kats took care of him, only for the villain to make a second attack against the building. The Blue Manx fighter features a highly advanced, female-voiced A.I. (Tress MacNeille) which teaches the Mega War II era pilot how to use its various modern functions that he's unused to. Seeing a cardboard cutout of Manx in the office, he mistakes it for the genuine article and shoots through the glass, terrifying Callie. The real Manx is down on the street and survives. Callie then gets back on the phone with Sinian.
Terrified at seeing his intended killer flying the jet named after his great grandfather, Manx attempts to drive himself to safety in his limo. Callie goes with him, explaining that Dr. Sinian told her only a descendant of the Manx family can put the Red Lynx back in his watery grave for good. She directs Manx to drive to the aircraft carrier from earlier so he can use the guns to shoot down the Blue Manx. The SWAT Kats engage the Red Lynx for a third time, but nothing they do seems to work, suggesting that Sinian was right; as the only living descendant of the Blue Manx, only the Mayor can kill the ghostly villain.
Manx is too afraid and can't keep his hands steady on the trigger, so he abandons the carrier's gun and tries to run a way. Razor shoots down on the Cyclotron and urges Manx to get on it with him while T-Bone runs interference in the Turbokat. Manx initially refuses, but Razor says if he doesn't kill the Red Lynx, he won't get reelected. Gathering his courage, Manx launches a missile from the Cyclotron, shooting the Blue Manx fighter down. It lands in the ocean and the Red Lynx is now presumably gone for good. Boasting that bravery is in his genes, Manx pins a "Vote Manx" button on Razor.
Tropes:
- Arc Words:Callie: How do you "kill" a ghost?
- Cool Plane: The Enforcers build a multi-million dollar jet called the Blue Manx, in honor of Mayor Manx's war pilot great grandfather, that is supposed to be designed to make the SWAT Kats' Turbokat obsolete. Unfortunately, the Red Lynx steals it when he loses his old plane. Manx destroys it to put an end to the Red Lynx for good.Manx: The Red Lynx?! In the Blue Manx?!!
- Fame Through Infamy: The Red Lynx may be considered "the most evil pilot in history", but Chance admires his piloting skills.
- The Only One Allowed to Defeat You: Mayor Manx is the Red Lynx's target because he is a descendant of the Blue Manx, the pilot who defeated him in Mega War II. The only way for this feud to end is if one of them dies. So even though the SWAT Kats shoot Red down the first time, he returned to continue his revenge, leaving Manx the only one that can kill him permanently.
- Took a Level in Badass: For all his talk about carrying his great grandfather's bravery, Manx finally makes good on the Blue Manx legacy in the end, if only to prove he's worthy of being re-elected thanks to Razor's encouragement.
- The Unreveal: Manx is running for reelection as mayor of Megakat City, though we never learn about his competition.
- Vengeful Ghost: The Red Lynx is brought back to life by some unknown force in order to take revenge on the Blue Manx, by going after his nearest living descendant: his cowardly great grandson Mayor Manx.
