Two grave robbers accidentally release the Pastmaster from his 800-year imprisonment within the Casket of the Ages. Disgusted with the modern era, he steals his spellbook, the Tome of Time, from the Megakat City Museum of History and attempts to magically transform the metropolis back to the medieval state he prefers. He summons dinosaurs through a magical time vortex to act as his bodyguards, one of whom knocks the Swat Kats through the portal and into the prehistoric era. Low on time and fuel, the Swat Kats must figure out a way to get back to the present-day Megakat City to stop the Pastmaster.
The swamp-dwelling Dr. Viper mutates his fellow evildoer Morbulus into a hulking bacteria blob following Morbulus' humiliating defeat by the Swat Kats. The bacteria monster then goes on a rampage through Megakat City, inconveniently dividing into two anytime it's hit. Viper's plan is for the monsters to break into the supposedly impenetrable Megakat Biochemical Labs and steal Katalyst 99, a rare biochemical compound he wants. With normal weapons ineffective against the giant bacteria, the Swat Kats quickly discover that the creatures have one weakness: electricity.
Criminal mastermind Dark Kat breaks into the Megakat Nuclear Plant and steals the components to build his ""doomsday device,"" a powerful nuclear bomb that he plans to drop on the city. Commander Feral sneaks aboard Dark Kat's ship, the Doomsday Express, in an effort to stop him, but is quickly captured. Lieutenant-Commander Steele, Feral's second in command, assumes control of the Enforcers, but would rather advance his career than rescue his boss. Thus, it's up to the Swat Kats to save both Feral and Megakat City.
The new, 300-story office building Megakat Towers is open for business, and Mayor Manx is trying to persuade foreign investor Mr. Young to house his corporate headquarters there. But Dr. Viper is back and he ruins Manx's plans as he seizes control of the tower with his army of acid-spitting ""plantimals."" He places a huge spore pod on the roof: when it explodes, it will shower Megakat City with spores, turning the metropolis into one big swamp (""Megaswamp City""). Obviously the Swat Kats won't allow this. While T-Bone runs interference in the Turbokat, Razor sneaks inside the building to stop Viper with the help of Callie Briggs, who happened to be inside when the building was taken.
The husband and wife gangster duo Mac and Molly Mange were thought to have died while trying to escape from Alkatraz. Now, for the first time since their ""makeover,"" courtesy of inventor Professor Hackle, they're back in Megakat City and planning to ""tear up this town like a scratchin' post!"" But Mac and Molly's first priority is getting revenge on those who had wronged them in the past, and at the top their hit list is Mayor Manx. It's mayhem down at City Hall as the Swat Kats fight to destroy the seemingly unstoppable Metallikats.
While in the middle of a battle against sea monsters who are attacking KatCo oil tankers, the Swat Kats become caught in of the Pastmaster's time portals, which appears out of nowhere and pulls them back into medieval times. There they find the evil wizard in the midst of laying siege to Megalith City, Megakat City's Dark Ages counterpart, with an army of mythological monsters (dragons, cyclopes, etc.) in an effort to force its ruler, Queen Callista, Callie Briggs' lookalike ancestor, to marry him. And that's not the only romantic complication! When Callista sees Razor pull a certain sword from a certain stone, she falls in love with him, causing T-Bone to become jealous.
Dark Kat enlists the assistance of technology thief and ""high-voltage low-life"" Hard Drive to destroy both the Swat Kats and their reputation as heroes. After the villains lure the vigilantes into a death trap in Dark Kat's hideout, Hard Drive uses the stolen Turbokat to pose as the Swat Kats and commit various crimes in order to frame them as criminals. Although T-Bone and Razor manage to free themselves, they find themselves pursued by the Enforcers for the crimes committed by Dark Kat and Hard Drive. With Callie's help, they must evade the Enforcers, clear their names, stop Dark Kat, and be back in time to tow a little old lady.
An accident with an experimental diamond mining machine, the Gemkat 6000, somehow turns brutal convict Rex Shard, into a crystalline giant whose touch turns people and objects to crystal. And that's only the beginning of his new powers. Seeking revenge for his accident, Shard first sets his sights on getting Warden Cyrus Meece, whose greedy exploitation of his prisoners led to the ordeal in the first place, and the Gemkat 6000's inventor, Dr. Greenbox, all the while randomly ""crystallizing"" every location he comes across. Can the SWAT Kats find a way to reverse Shard's condition before it's too late?
The vengeful spirit of the Red Lynx, Mega War II air ace and the most evil pilot in aviation history, returns from his watery grave after his sunken biplane is found by dockworker and war veteran Abner Doolittle, intending to hunt down and kill the only living descendant of the flier who put him there, the Blue Manx. Said descendant is, of course, none other than Mayor Manx. Can even the Swat Kats shoot down the Red Lynx? And can Mayor Manx overcome his cowardice even to save his own life? He'll have to, especially once the ever-helpful Dr. Sinian discovers that only a relative of the Blue Manx, such as the Mayor, can destroy the Red Lynx for good.
Professor Hackle intends to reprogram the Metallikats to be good, but Mac and Molly escape from his lab before he can. In search of their armored hovercraft, the Metallikat Express, they wind up in the salvage yard near Jake 'n' Chance's Garage. There, they inadvertently discover the hidden Swat Kats hangar and thus uncover the secret identities of the vigilantes themselves! Chance and Jake, in their civvies, must defend their own base from the murderous, mechanical gangsters. Although their bodies are destroyed, the Metallikats survive as disembodied heads crawling around on spiderlike legs, and eventually take control of two Puma-Dyne Macrobots, giant and powerful space exploration robots, and begin to trash the city. Now, the Swat Kats must stop the Metallikats from revealing their secret and save the city!
Hitching a ride aboard the deep space probe Kat Sat 1, cicada-like aliens with pointed, cat-like ears take over the M.A.S.A. Space Center, biting the Kat Sat 1's creator, astronomer Dr. Harley Street, and others, turning them into literally bug-eyed slaves as part of their plan for world conquest. Ann Gora, seeking an interview with Dr. Street regarding the success of the Kat Sat 1, stumbles onto their plans and is quick to alert the authorities. It's up to the SWAT Kats (who else?) to thwart the invasion, with poor T-Bone fighting his fear of bugs every step of the way.
Comedian Lenny Ringtail, whose mind snapped after he lost the title of ""King of Late Night"" to his rival David Litterbin, allows himself to be possessed by the ghost of Madkat, a jester who suffered a similar rejection hundreds of years ago. The result is a wisecracking, shapeshifting harlequin who uses his magical powers to kidnap the ""King,"" ""Queen,"" ""Knight"" and ""Jester,"" or Mayor Manx, Callie Briggs, Commander Feral and Litterbin, respectively, imprisoning all but Callie within a magic puzzle box and vanishing into thin air before the Swat Kats can stop him. Can they find his weakness in time to save Callie?
After being beaten by the Swat Kats because they were too busy fighting each other, Dark Kat and Dr. Viper decide to team up and unite against their common enemies. They recruit the Metallikats to their cause, forming the Invincible Alliance of Evil, whose only purpose is to kill the Swat Kats once and for all. Kidnapping Mayor Manx and Callie, the villains give the Swat Kats an ultimateum - surrender by sunrise or risk the deaths of the hostages. Can the Swat Kats find a way to rescue Manx and Callie without giving themselves up? And will Commander Feral lend a helping hand?
Dr. Viper floods Megakat City with Katalyst X-63, a ""hideous mutating ooze"" that turns normal animals into giant monsters. With the city submerged in slime and infested by huge, repulsive mutants, the Swat Kats must undertake a perilous mission to Megakat Biochemical Labs, where they must retrieve the antimutagens needed to restore everything to normal. T-Bone, who can't swim, nearly drowns in the slime, and later becomes a mutant himself when one of the creatures bites him. Worse, Dr. Viper eventually uses the katalyst on himself, turning into a skyscraper-sized monstrosity.
The Pastmaster returns and sends the Swat Kats through one of his time portals and into Megakat City's future, where Mac and Molly Mange rule a nightmare world of killer robots (called ""Metallitack Units""), confining ""non-metallic creatures"" to slave labor camps, and the vigilantes' friends are rebel freedom-fighters. But the worst part is that the Swat Kats' future selves are dead, killed by the Metallikats when they took over. Now, it's up to the pilots from the past to set things right. But when the older Callie and Mayor Manx are kidnapped by the Metallitack Units, the Swat Kats form an uneasy alliance with the Pastmaster, who wants revenge against Mac and Molly for doublecrossing him. Together with Commander Feral and Felina, they storm Metallikat Headquarters.
A group of alien space pirates, led by the evil Mutilor, arrive over the skies of Megakat City, planning to drain the planet's water using a ship stolen from a peaceful race of cat-like aliens called the Aquians, to sell to another race of aliens altogether, the Zarhabi. With the Turbokat still in repairs, the Swat Kats must employ other methods of battling against the invaders to defend their world.
Razor's self-confidence is shattered when he believes he has injured two elderly civilians during the Swat Kats' pursuit of Dark Kat. Discouraged, he quits the team, leaving T-Bone to face Dark Kat's latest evil plot alone. This time around, the criminal mastermind plans to destroy Megakat City with his robotic spider craft, the Black Widow, which grows bigger whenever it absorbs power! Can T-Bone succeed on his own, or will Razor regain his confidence and return to the SwatKats?
A new villain, Turmoil, attempts to seize control of the skies over Megakat City and ransom their use for the ""paltry sum"" of $2 million in gold each week. Backing her up is the Omega Squadron, her own private air force comprised entirely of female pilots, as well as the Vertigo Beam, a powerful ray cannon that causes pilots to become disoriented and crash. Obviously the Swat Kats are having none of this nonsense. When T-Bone both outflies the Omega Squadron and successfully recovers from the effects of the Vertigo Beam, Turmoil is impressed. She attempts to persuade him to join her side, and, truly remarkably, he accepts; first, though, he must prove his loyalty... by killing Razor!
A hyena-like villain named Chopshop (voiced by Nick Chinlund) is being pursued by the SWAT Kats in his highly advanced helicopter. After a brief but intense aerial dogfight, the SWAT Kats manage to subdue Chopshop and hand him over to the Enforcers. Ann Gora interviews them and Razor comments on having the help of their high-tech gadgetry. Meanwhile, Hard Drive has somehow escaped and steals a recently invented anti-weapons scrambler from Pumadyne scientist Dr. Ohm. With this, Hard Drive prepares to steal the gold being transferred from the Megakat Mint to the City's banks on the newly constructed Megakat Railway. The SWAT Kats come to stop him, but all of their weapons are disabled by the weapons scramber. It is up to T-Bone and Razor to outwit rather than outgun their opponent and retrieve the gold.
An archaeological expedition led by Dr. Abby Sinian in search of the Lost Pyramid of Katchu Pitchu instead encounters the Pastmaster, who unearths the pyramid by himself using the equally long-lost Jeweled Headdress of Katchu Pitchu in order to reanimate the dead monarch's army of giant mummy warriors. He sends them to destroy Megakat City and kill Mayor Manx, but when one of them knocks off Callie Briggs' glasses, he notices her resemblance to to his beloved Queen Callista. He soon abducts her and tries to force her to marry him, and only the Swat Kats can stop him, aided by a friendly robot named Cybertron given to them by Professor Hackle.
The Megakat Metallurgical Company has some problems: several of their miners have gone missing deep in the company's agracite mines. The Enforcers are called in to investigate by Taylor, the company's mining foreman, with Ann Gora tagging along incognito as a miner. When she too disappears, it's up to the Swat Kats, with help from Lt. Felina Feral, to enter the mines and find her. They soon discover the root of the problem, too - a horde of giant scorpions mutated by toxic waste that was illegally dumped by Megakat Metallurgical's president, Tiger Conklin.
Mayor Manx and Mr. Young plan to build an industrial park on tropical Anakata Island, but a bulldozer accidentally plows into and breaks breaks the sacred Talisman Stone, which is said to keep the demon Volcanus asleep within the island's central volcano. Naturally, the beast is soon set free and heads towards the mainland with the intent of smashing everything in sight. Only the Swat Kats can stop him, but Volcanus is impervious to almost everything! Can he be stopped before he destroys the Megakat Nuclear Plant?
Dr. N. Zyme and Dr. Elrod Purvis engineer Viper Mutagen 368, a regenerative growth formula. Zyme imagines the benefits of the mutagen to mankind and tells Purvis he could not have done it without him. Purvis is uncaring, and only wants to sell the mutagen to the highest bidder and become rich. Zyme leaves the lab and Purvis steals the mutagen and its research for himself, only to be discovered by Zyme and pursued into the building's stairwell. Purvis trips down the stairs and becomes covered in the growth formula. He then collapses, supposedly dead and is taken to the morgue. Dr. Zyme discovers that the mutagen is ineffective and mutates its host into an evil monstrosity. Purvis is mutated by the formula and becomes Dr. Viper, taking his name from the mutagen itself. He then proceeds to apply the mutagen to mosquitos and honey bees to attack those responsible for his mutation.
A stray lightening bolt hits the Turbokat while the Swat Kats are testing their new dimensional radar system, which results in them being hurled into an alternate dimension where evil versions of themselves are not only wanted for just about every crime in Megakat City, but are also working for Dark Kat. Mistaken for the Dark Swat Kats by Dark Kat, T-Bone and Razor are sent to Puma-Dyne to steal the Mega-Detonator, a key component for an implosion bomb which the criminal mastermind plans to use to destroy Enforcer Headquarters. When Dark Kat realizes he's been had, he sends the real Dark Swat Kats to kill their good counterparts and acquire the Mega-Detonator. Making things even more complicated for the vigilante duo are the fact that Callie Briggs is also evil and in on Dark Kat's plot, but the Enforcers mistake them for the Dark Swat Kats and are after them, too.
The Swat Kats stop the Metallikats from robbing the Megakat City Mint, and in the process the two robot gangsters are severely injured, Molly moreso than Mac. When Mac finds out about Dr. Lieter Greenbox's new invention, the Micro-Brain Repair Unit which can fix anything, he immediately takes himself and Molly to Greenbox's lab and steals the device. The Metallikats use it to repair themselves, but in the process the device becomes contaminated by their criminal programming. Achieving sentience, it names itself Zed and proceeds to go on a citywide rampage, assimilating all manner of metal and machinery (including Mac!) onto itself, constructing an ever-growing armored shell. Naturally, only the Swat Kats can stop Zed, with some help from a vengeful Molly. Unfortunately, Zed's next stop is Puma-Dyne, where it plans to get its hands on the Mega-Beam laser weapon. Worse, Greenbox has become so impressed by what his genius has wrought that he's gone completely looney-tunes and is doing eve
The finale of the Swat Kats series finally arrives, as Ann Gora, Tiger Shark, and Tom Cat, report on all the historical adventures of the Swat Kats. T-Bone and Razor are highlighted in several instances with the numerous weapons and vehicles they operate, along with certian maneuvers they perform to get away from trouble. During the show, several questions are mentioned in the SKIQ, The Swat Kats Inside Quiz. Subjects include a multiple choice Q and A with a situation pops out, a situation based exam on what you would do if you were the Swat Kats, and then a segement called "Name That Villan".