A pair of archaeologists in Africa are examining the remains of prehistoric men. Behind them, the mountain disappears, revealing a cloaked Gorilla City, as a gorilla on a hover bike speeds out of the city while being pursued by other gorillas. However, the gorilla escapes his pursuers, who are forced to retreat back into the city after seeing the archaeologists.
In Central City, the Flash is showing off to two uninterested ladies until he sees a runaway van shoving aside cars heedlessly. The Flash chases after the van, while one of its passengers attempts to shoot at him with a futuristic pistol. The chase ends at a bridge, where the van and its occupants are captured by Green Lantern, who has arrive to assist the Flash. They find the van was carrying stolen radioactive isotopes and the drivers are research scientists at the institute from which the isotopes were stolen. Strangely, the scientists seem to wake up and claim to have not to remember what they were doing.
Flash and Green Lantern arrive at the institute to question the scientists colleague, Dr. Sarah Corwin, who states that she has no explanation for their behavior. While she speaks to Lantern, Flash notices a familiar gorilla among the labs test monkeys. The heroes then hear an unusual report of a gorilla driving a getaway car to escape the police. Flash manage to chase down the car and is surprised when the gorilla speaks. Suddenly, Corwin, hiding on a rooftop, blasts Flash with some kind of energy ray.
Flash has a series of bizarre hallucinations, then wakes up inside a jail cell. The police show him a surveillance tape of him stealing the isotopes from the police impound. His interrogation is cut short by the arrival of Lantern, who has paid Flash's bail to take him away, then angrily subjects Flash to another interrogation. Flash insists that hes innocent, and cant explain why he was stealing the isotopes. The last thing he can remember is stopping the talking gorilla.
Lantern is skeptical, but gives Flash the benefit of the doubt as they manage to track the gorilla down. The gorilla introduces himself as Solovar, chief of security for Gorilla City, a civilization of hyper-intelligent gorillas hidden from mankind. Their city has been peaceful until recently, when Grodd, a genius scientist, went rogue and developed a mind control helmet that he tried to use to take over the other gorillas. The authorities developed a resistance to the helmet and chased Grodd out, but now he's sworn revenge on the city. Solovar also says his investigation has found an email correspondence between Grodd and Corwin. Needing no further information, Flash streaks back to the institute, before Solovar can explain that he has a small supply of electronic headbands that will shield a person from Grodds mind control. By the time he and Lantern get to the institute, Grodd has already subdued Flash and placed him under mental control, and uses him to attack Lantern. Lantern knocks Flash out with difficulty, but Grodd and Corwin have escaped. Grodd has used the isotopes to power a machine in the heart of Central City, which he activates before he and Corwin speed away on his hover bike. Lantern and Solovar run to the machine, but then it gives off a colossal energy surge, like an explosion, that covers Central City and leaves nothing behind.
Green Lantern, Flash, and Solovar awake to find that Central City is covered in an invisible, impenetrable dome similar to Gorilla City's. The trio made their way into Central City and find Grodd holding court in the city square, with a crowd of people under his mind control. Lantern, Flash, and Solovar confront him, but Grodd sics his puppets on them, before fleeing with Corwin. The three escape the mob and track Grodd to a military base, where Grodd fires four nuclear missiles at Gorilla City. Green Lantern flies after the missiles, while Flash and Solovar deal with Grodd.
Meanwhile, the Justice League detect and investigate the disturbance in Central City. Soon they identify similar energy readings from Gorilla City, where they arrive, but are immediately captured by the city's security forces, who believe they are spies from the outside. Fortunately, the League break out of their imprisonment but are trapped by the shield. As they are being cornered by the security forces, the shield suddenly malfunctions and shuts down Grodd left a sabotage device behind. At the same time, the gorillas detect the incoming missiles. To their surprise, the League offers to help them.
Green Lantern is able to neutralize two of the missiles, but debris from one of the missiles briefly knocks him out. As the remaining missiles are almost close to Gorilla City, the other Leaguers are awaiting. J'onn phases out the guidance system on one, causing it to crash harmlessly. Hawkgirl smashes the last missile with her mace, breaking it into pieces, but the warhead stage is still heading for the city. Wonder Woman flies into the missile's path and stops it from exploding, but she is crushed underneath it before it grinds to a stop. The normally stoic Batman furiously dig in the rubble under the missile, shouting Wonder Woman's name. When there is no response, he gives up, but then the missile body lifts, and Wonder Woman emerges, holding the guidance system. The city is safe. Wonder Woman realizes Batman's attempt to save her and kisses him on the cheek.
Grodd is angered that his plans are foiled and goes berserk and attacks Flash while Solovar is temporarily subdued. Flash is able to dodge his attacks at ease, but he then proposes a fair fight, and takes off his headband (despite Solovar's protests), inviting Grodd to take off his helmet. Grodd, of course, does no such thing. He activates his helmet but screams as it feeds back on itself, due to some subtle sabotage by Flash when he patted it down over Grodd's eyes. To his surprise, Corwin turns out to have not been under Grodds mind control instead, she had genuinely fallen in love with him.
The League meets up in Gorilla City, where the leaders thank them for their help. Solovar shows them Grodd, now a brain-dead vegetable, bearing an almost comic resemblance to a zoo ape. However, as the League and Solovar walk away, the vacant look in Grodds eyes disappears, and they narrow with hatred...
- Arbitrary Skepticism: Green Lantern is skeptical of Flash's claims that Solovar could talk and drive a car.Green Lantern: I'm expected to believe this?
Flash: Hey, we've both got a Martian's phone number on our speed dial! I think I deserve the benefit of the doubt here.
- Batman Gambit: By Flash of all people on Grodd. He anticipated Grodd would not honor a fair fight if he took off his protective headband, so he tricks him into doing it after Flash secretly rewired his mind-control device from his previous tussle with him.
- Cliffhanger Copout: The end of Part One has Grodd's machine give off an explosion-like energy surge that seemingly reduces Central City to a crater. The opening of Part Two reveals that Central City is actually under a dome similar to Gorilla City's and that the "crater" is actually an illusion meant to fool outsiders.
- Does Not Like Spam: Grodd hates bananas.
- The End... Or Is It?: After the Leaguers leave, Grodd's blank expression from being mind-wiped turns into one of pure rage.
- Hidden Depths: The Flash's intuitiveness is commented on by a surprised Green Lantern.
- I Take Offense to That Last One!:Gorilla Grodd: Humans are slow, ugly, immoral, and have an unpleasant body odor!Flash: Hey, who you calling slow?
- Interspecies Romance: Grodd and Corwin.
- It Works Better with Bullets: This is how Flash defeats Grodd.
- Lame Comeback: Flash to Grodd: "Oh yeah? Well, you're... naked!" He actually shrugs to Solovar behind him because he knew it was lame.
- Lost World: Gorilla City is this trope.
- Mass Hypnosis: Gorilla Grodd controls the populace of Central City with his mind-control helmet as part of his Evil Plan.
- Mythology Gag: Flash's hallucination sequence features several references to various covers of different Flash/Barry Allen comics.
- The "good cop" interrogating Flash looks like Barry.
- Not Brainwashed: Dr. Sarah Corwin.
- Omnicidal Maniac: Grodd, as always.
- Present Company Excluded: When Green Lantern suggests calling for backup from the rest of the League to help with Grodd, Flash asks him if the two of them cannot take down a dumb gorilla, quickly adding "No offense" to Solovar, who was with them.
- Ship Tease: This two-parter episode marked the first indisputable example for Batman and Wonder Woman, where he desperately tries to dig her out of the rubble while calling out her name, and her pecking him on the cheek in gratitude when she notices his dirty hands. Interestingly, Word of God is that it was originally written as concern for a friend. However, after the fanbase latched onto it, Bruce Timm decided to amp up later moments (despite the Foregone Conclusion that is Batman Beyond).
- Self-Restraint: Shown by Flash after he's arrested; as Green Lantern tells the police, they could never have held him with a pair of handcuffs had he wanted to escape.
- Smile of Approval: One of the gorillas who accused the heroes of being spies gives a smile at them for stopping the missiles from destroying Gorilla City.
- Smug Super: Flash is boastful of his accomplishments while trying to woo a couple of women. They are less than impressed, at least until he swings into action when a wildly swerving truck almost gets them hurt.
- You Watch Too Much X: This exchange:Flash: Usually, when a city looks this empty, flesh-eating zombies are involved.Green Lantern: You watch too many movies.Solovar: Shh! Listen.(sound of a crowd chanting Grodd's name)Flash: Maybe you don't watch enough.