An evil pilot named Morbulus (Jim Cummings) flying a purple jet blows up an oil refinery. Hot in pursuit are the SWAT Kats. Their enemy has been blowing up refineries all day. Razor targets the other jet with an Octopus Missile, but Morbulus dodges, allowing the missile to instead hit the upper floor of a building. It turns out this is because Morbulus literally has a second pair of eyes in the back of his head, allowing him to see behind as well as in front of himself. As he prepares to bomb another refinery, T-Bone flies the Turbokat into a cloud bank. Using it as cover, he maneuvers underneath Morbulus' jet where even he can't see them. A Cookie-Cutter Missile fired by Razor cuts the villain out of his cockpit, and he is saved from falling to his death by the Turbokat's "Sky Claw," after which the SWAT Kats drop him in the ocean and fly away.
When Callie Briggs and Commander Feral arrive, they fish what they think is Morbulus' drowned body out of the ocean, but it turns out to just be his empty clothes put back together to make it look like he's still in them. He's escaped. Mayor Manx arrives with a group of reporters, including Ann Gora (Candi Milo) from Kat's Eye News. As they interview Feral, Morbulus, in his underwear, comes ashore further down the beach and enters a drain pipe where he encounters half kat, half snake evil biochemist Dr. Viper (Frank Welker).
The SWAT Kats return to their secret hangar underneath the Megakat City Salvage Yard, changing back into their civilian identities as mechanics Chance Furlong and Jake Clawson. They're shocked when they turn on the news to discover that Morbulus has escaped. When Commander Feral angrily blames them, Chance throws a can of milk at the screen, breaking the TV. Callie shows up to get her car's engine looked at. She turns down Chance's offer to drive her home in the tow truck, explaining that Mayor Manx's chauffeur is waiting outside in the limo, and departs despite Chance's attempts to flirt with her.
Meanwhile, in an area of the swamp known as the Dead Forest, Dr. Viper has taken Morbulus back to his secret lair, where he explains he needs a biochemical compound called Katalyst 99. Morbulus initially agrees to help him get it, but balks when told it's in the "impenetrable" Megakat Biochemical Labs. Undeterred, Viper puts a drop of purple liquid onto Morbulus' arm, causing him to painfully mutate into the scientist's newest creation, a giant bacteria monster. Viper promises to use him to steal Katalyst 99 and destroy Megakat City.
The following day, Chance installs "turbo plugs" in Callie's engine to give the car extra horsepower, over Jake's objections. When he revs the engine, the extra power causes it to blow up. Now they need a new engine and a new TV. Their ne'er-do-well co-workers Burke (Mark Hamill) and Murray (Charlie Adler) show up to dump off a load of scrap. In the scrap they brought, Chance and Jake find a TV and an automobile engine they can use.
Meanwhile, Dr. Viper and his slimy purple bacteria monster stop off at a farm. Because Morbulus had eyes in the back of his head, the creature he's become has four eyes. After the monster eats a cow, the farmer (Mark Hamill) tries to fend it off with his pitchfork, but Viper grabs him with his prehensile tail and feeds him to the creature before he leads his creation into the city, where it attacks the opening of the new Manx Municipal Park, endangering Callie and Manx.
Trying to escape in Manx's limo, Callie drives into and through the monster, causing it to divide like an amoeba into two monsters. Since Kat's Eye News was covering the park opening, Chance and Jake witness the attack on their new TV while installing the new engine in Callie's car. Becoming T-Bone and Razor again, they fly off in the Turbokat, although it's actually Commander Feral who rescues Callie and the Mayor in his helicopter as the monsters eat the limousine.
Not listening to Callie or the SWAT Kats, Feral orders his pilot to fire on one of the monsters, but all this does is make it divide again, creating three creatures. The trio head towards Megakat Labs as Callie, Manx and Feral race ahead in the chopper to beat them there. One of the bacteria monsters deviates from Viper's plan and wanders into a subway tunnel. Razor follows it on the Cyclotron, but is too late to stop it from eating an entire subway train full of innocent people.
Razor discovers how to kill the bacteria monsters when the creature, attempting to pursue him, steps on the subway's third rail and is electrocuted, melting into lifeless brown glop. Meanwhile, at Megakat Labs, Callie, Manx, Feral and the Enforcer pilot seek the help of biochemist Dr. N. Zyme (Paul Eiding), who identifies the monsters as giant bacteria and proposes to use a high dose of antibiotics to kill them. He then assures a worried Callie that the lab's windows are made of unbreakable armored glass. Outside, the remaining bacteria monsters arrive and smash the building's defenses, allowing Dr. Viper to just walk inside.
On the roof, Dr. Zyme loads a missile containing antibiotics onto Feral's chopper. Manx comes with Feral, refusing to stay behind in case Zyme's plan fails. The SWAT Kats arrive and kill one of the remaining monsters using a Megavolt Missile, which electrocutes it. Observing this from his chopper, Feral fires Zyme's antibiotic missile at the final monster, but it fails. Appearing inside the main lab, Viper taunts Callie and Dr. Zyme, explaining that he made his bacteria monsters immune to antibiotics. Despite Zyme's earlier claims, the bacteria monster smashes the lab window in. Zyme gets grabbed as the monster's hand comes down over him, while Viper takes Callie prisoner by grabbing her with his tail and gathers up armfuls of Katalyst 99.
The SWAT Kats lure the final bacteria monster onto a metal bridge with powerlines running over it, and cut the lines just as the creature passes under it. The downed lines fall onto and electrocute the last of Viper's monsters, killing it. They then fly back to Megakat Biochemical Labs, where they confront Viper, making him drop Callie. Unwilling to surrender, the evil scientist shakes up the containers of Katalyst 99, which turn out to be highly volatile; they explode when thrown, starting a huge fire. Before the flames can reach a store of flammable chemicals, the SWAT Kats and Callie fly safely away in the Turbokat as the building blows up, seemingly killing Dr. Viper.
After depositing Callie safely on the street, the SWAT Kats are yelled at Feral for cutting half the power to Megakat City when they severed the powerlines. T-Bone simply replies that if he knows a better way to "cook a giant bacteria," he should let them know. The SWAT Kats fly away, having a good chuckle at the sight of Burke and Murray having to clean up all the melted bacteria remains with a bulldozer.
Tropes featured in this episode include:
- Aborted Arc: Chance's interest in Callie, and the implied Love Triangle with them and Jake. It never comes up again, because this episode ended up being the only time that Callie interacts with the SWAT Kats as Chance and Jake. The only other episode that even alludes to their acquaintance is "Night of the Dark Kat." This would be a case of Early Installment Weirdness except for the fact "Succubus!" would've picked it up again.
- Antagonist Title: The "giant bacteria" is/are the main threat of the episode.
- Artistic License Chemistry: A catalyst is just something that causes a chemical reaction, but "katalysts" are explicitly referred to as biochemical compounds.
- Artistic License Biology: Dr. Viper takes a (more or less) ordinary kat, a feline, and transforms him into a giant globby germ monster, completely changing his physiology.
- Artistic License Physics: Morbulus comes to no harm despite being grabbed out of free fall with the Sky Claw, when in reality, a stop that sudden would've broken his neck.
- Ash Face: Jake after the car engine explodes in his face.
- Baleful Polymorph: Morbulus. From kat to slimy purple Blob Monster.
- Big Damn Heroes: The SWAT Kats rescuing Callie from Viper's coils by flying the jet through the armored glass windows of the lab, forcing the villain to drop his prisoner and get sent flying back into the wall.
- Big "NO!": Morbulus' final intelligible dialogue as he's transforming. Viper counters with a Big "YES!".
- Body Horror: Morbulus' mutation, particularly the part where the eyes on the back of his head move up to the front.
- Bus Full of Innocents: One of the monsters eats an entire subway train full of helpless kats.
- By the Lights of Their Eyes: How Viper is introduced, with his Glowing Eyes of Doom shining out from inside the drain pipe.
- Dangerous Windows: The lab windows, despite Zyme's assurances to Callie that they can't be broken.
- Darker and Edgier: Compared to "The Pastmaster Always Rings Twice," this episode is exceptionally more violent and features a pretty horrific mutation scene for the time and several deaths. This is a bit of an inversion, though, because "The Giant Bacteria" was made first, and so but for the order in which they were aired it's less that "The Giant Bacteria" is Darker and Edgier and more that "The Pastmaster Always Rings Twice" is Lighter and Softer.
- Death by Looking Up: Dr. Zyme just stands there and screams as the bacteria monster's hand reaches down for him.
- Dirty Coward: Manx knocking Callie off the rescue ladder. Lampshaded by Feral later ("You're a coward, Manx!").
- Discretion Shot: How the episode handles the farmer's death. We don't even see the shadow of him being eaten like we did with the cow; the bacteria monster's body blocks our view of even that.
- Disproportionate Retribution: The reason Viper feeds the farmer to the bacteria monster is because he tried to defend himself from the creature using his pitchfork. Apparently this counts as meddling.Viper: I'll teach you to tamper with my experiment!
- Does This Remind You of Anything?: Dr. Viper seems to enjoy Morbulus' mutation a little too much, almost as if it is turning him on ("YYYESSSSS!").
- Early Installment Weirdness: Although Ann Gora appears, it's two different, male reporters who interview Feral at the refinery and on TV later.
- Establishing Character Moment: Several, this being the very first episode written and produced, despite the second aired:
- Chance smashes the TV when Feral blames them for letting Morbulus get away, showing us that he has a temper problem. His attempts to flirt with Callie also demonstrate that he sees himself as something of a Lothario (it's Played for Laughs).
- When Razor misses Morbulus, T-Bone asks, "How'd you miss him, sureshot?" This is meant to set up that Razor has Improbable Aiming Skills (making he fact the missed/Morbulus dodged unusual).
- As Jake he expresses subdued annoyance at Chance breaking the TV, showing us he is more even-tempered than his companion.
- Razor's horror at the subway train being eaten is the first indication that he doesn't like it when innocent bystanders are hurt or killed.
- Feral blames the SWAT Kats for Morbulus' escape, more firmly establishing that he thinks that they're reckless and irresponsible. He also ignores both them and Callie later, doubling down on the previous episode setting him up as ignoring those who he perceives as challenging his authority.
- The episode is one big Establishing Character Moment for its main villain, Dr. Viper. He betrays and mutates Morbulus and finds his suffering immensely enjoyable and then gleefully murders an innocent farmer by feeding him to the monster. These acts establish Viper as a sadist who delights in the pain and misery of others.
- Burke and Murray show up, are jerks and drive off, quickly and efficiently letting the audience know what they're all about.
- Explosive Overclocking: When Chance puts "turboplugs" into the engine of Callie's car, it gives the engine extra horsepower. But Chance keeps revving the engine, causing the engine to overload and blow to bits.
- Extra Eyes/Eyes Do Not Belong There: Morbulus' defining characteristic is that he has eyes in the back of his head.
- Extreme Omnivore: The bacteria monsters pretty much cram whatever they can grab into their mouths without hesitation. Kats, cars, you name it.
- Family-Unfriendly Death: The three bacteria monsters' deaths are pretty horrific, especially the final one, the way it convulses as it's electrocuted.
- A Glass in the Hand: Twice. First, when enraged over Feral badmouthing them on the news, Chance squeezes his can of milk before throwing at the TV screen. Later, he snaps the pencil Murray gave him.
- Gratuitous Laboratory Flasks: Viper's lair in the Dead Forest is chalk full of them. A bunch of beakers, flasks and retorts bubbling away over Bunsen burners, none of which Viper actually appears to use for anything.Viper: Quite an "eyeful," isssn't it, Morbulusss?Morbulus: Very impressive. Looks like you've got everything a mad scientist needs right here.
- Hellish Copter: Morbulus shoots down three Enforcer choppers at the beginning.
- High-Voltage Death: The only thing the bacteria monsters are vulnerable to is heat, and the best way to deliver said heat is by frying them with electricity.
- Hydra Problem: Sort of. Due to the limitations imposed by the eye number, the monsters can presumably only potentially divide a total of three times to create four monsters.
- In Medias Res: The episode begins with Morbulus' "refinery reign of terror" having already gone on for some time.
- Jerkass Has a Point: Feral when blaming the SWAT Kats for letting Morbulus get away because they dunked the guy in the ocean for their own amusement.Feral: If they'd held Morbulus until we arrived, he'd be in custody right now!
- Just Plane Wrong: Somehow, helicopters can keep up with fighter jets in this universe.
- Love Triangle: Chance is interested in Callie, but she doesn't really seem to reciprocate, and when she leaves, she makes a point of flirtatiously saying goodbye to Jake, not Chance. It's possible she does like Chance back, and only did this to make him jealous. note
- Mad Scientist: Dr. Viper is flat-out referred to as one, and he seems to take it as a compliment.
- Made of Explodium: Katalyst 99. Viper shakes it up, throws it, and kaboom! Megakat Biochemical goes up in flames.
- Me's a Crowd / Self-Duplication: How the bacteria monster's "reproduce." Whenever one is hit, it splits in two like an amoeba. However it can only do this three times because there can only be as many monsters are there are eyes.
- Mega-Microbes: The main threat of the episode.
- Never My Fault: The SWAT Kats, Chance in particular, refuse to accept blame for Morbulus getting away.
- Off-Model: From this point on in the series until "Night of the Dark Kat," the show's animation isn't very good. Feral in particular suffers in this episode, with Conjoined Eyes in some scenes.
- Phlebotinum Overdose: The "turboplugs" Chance uses on Callie's car cause the engine to overheat and blow up.
- Prehensile Tail: Dr. Viper, being part snake, has a prehensile tail. He uses it to grab people.
- Riding into the Sunset: Well, sunrise, but whatever.
- Save the Villain: The SWAT Kats save Morbulus from falling to his death after he's cut out of his jet, grabbing him out of the air with the Sky Claw.
- Scream Discretion Shot: During the final stages of Morbulus' transformation, it cuts to the outside of Viper's Supervillain Lair and all we hear is his final gurgling scream.
- Shadow Discretion Shot: When the monster eats the cow, all we see is the shadow cast against the barn wall. This is also the case with the farmer, but only when Viper picks him up with his tail and holds him out for the monster to eat - the episode goes one step further and also has the creature's body block the shadow when the farmer actually gets eaten.
- Shoot The TV: Chance throws a can on the TV in anger for Feral calling the SWAT Kats out for letting Morbulus escape.Jake: Great, first Morbulus is gone and so is our TV!
- Slasher Smile: For whatever reason, the bacteria monsters always have huge, open-mouthed grins. The only time one of them doesn't grin is right before it dies via Megavolt Missile.
- Soft Water: Morbulus' "mega belly flop" into the ocean leaves him none the worse for wear.
- Swamps Are Evil: Dr. Viper lives in the creepiest part of Megakat Swamp, the appropriately-named Dead Forest.
- Taking You with Me: Viper blows up Megakat Biochemical Labs with himself, Callie and the SWAT Kats still inside rather than surrender.
- Tempting Fate: Dr. Zyme assures Callie that the lab windows are incapable of being broken. No prizes for guessing what happens a few minutes later.
- Throwing the Distraction: How Morbulus gets away, with some elements of Giving Them the Strip. While he's in the water, he takes off his clothes and puts them back together to make it look like he's still in them, them swims to safety while the Enforcers fish his "body" out.
- Ungrateful Bastard: Manx. Callie saved him, and he "thanks" her by knocking her off the helicopter's rescue ladder.
- Uncertain Doom: Dr. Zyme. It cuts away just before he would've been grabbed and the episode never confirms or denies whether the monster got him. Not helping matters is the fact the the creature appears to get distracted by Feral's chopper. Zyme just disappears and is never mentioned again.
- Unwitting Instigator of Doom: The SWAT Kats for not holding on to Morbulus and Callie for causing the bacteria monster to divide for the first time. In Callie's defense, she couldn't have known that the creature was able to divide.
- What Happened to the Mouse?: In most versions aired on Cartoon Network and Boomerang, the farmer's death scene is cut, so he simply vanishes after reacting to the monster eating his cow. The DVD edits the scene back in, and most recent reruns have followed suit.
- What the Hell, Hero?: Feral calls the SWAT Kats out for letting Morbulus get away, but is pretty much ignored, and even the episode itself treats him as wrong. Mostly because he always has it in for the SWAT Kats.