"Viper" opens with young Bruce Wayne piecing together the mystery of his parents' death in Wayne Manor. Alfred, ever the concerned servant, wonders aloud if Bruce's quest for revenge will ever succeed. Bruce says his work is not hinged on revenge, but learning how Gotham works as a city. Specifically, he wants to know how Wayne Enterprises is connected to the Arkham Project and Gotham's crime families. Although still a child, Bruce possesses the detective prowess and obsessive dedication that will define his future as The Dark Knight.
Meanwhile, a street guitarist is slipped a vile of green liquid from a stranger. The player, asking no questions, opens the vial and inhales its fumes. Its effects on the guitarist are instantaneous, turning his skin pale while stretching a heinous grin crosses his face. Feeling this newfound power, the guitarist walks into a boedga and chugs a gallon of milk from the jug. When confronted by the clerk, the man growls "Don't vex me, mortal." Breaking the owner's bat with his bare hands, the guitarist beats the storeowner senseless and rips his ATM straight from the walls.
When nearby Gordon and Bullock hear the bodega's alarms, they rush inside. Luckily, the entire incident was caught on security footage, giving them a face to identify. After canvassing through Gotham, Gordon discovers the guitarist's name, Benny, and where they can find him.
Even though they locate Benny, still high on Viper and with dozens of empty milk gallons, Gordon and Bullock can't get the answers they're looking for. While Benny tries throwing the ATM at the duo, his skeleton breaks down into pebbles. As Gordon and Bullock scratch their heads over the bizarre development, Benny's Viper provider strolls the streets of Gotham handing the same vials like free candy.
After testing a sample of Viper, Edward Nygma deduces that Viper burns on a victim's calcium levels, explaining the unquenchable thirst for milk, and the skeleton's eventual disintegration.
Tracing Viper's chemicals, Gordon and Bullock hone in on Viper's origins at the WelZyn chemical company. The creator is Stan Putolski, an ex-chemist with an axe to grind against his former employers at WelZyn.
Meanwhile, the escalating turf war between Maroni and Falcone heats up. While Falcone and Fish meet with their Russian contact for ways to turn the Arkham deal against Maroni, Maroni hatches a plan with Penguin to overthrow Falcone's casino.
And how does Maroni reward this potential partnership? By stringing Penguin up until he can prove Penguin's trustworthiness. As the only one who can verify Cobblepot’s story, Gordon is forced into a sit-down with the Don. Gordon gives a truthful recount of his history with Penguin, saving his and Penguin's. Gordon gives an honest summary of his involvement with the Wayne conspiracy. But before Gordon leaves, Maroni makes it clear that he knows Gordon's secret with Cobblepot, and won't be afraid to extort it in the future.
Back at the Gotham MCU, Gordon and Bullock locate Potolsky's old co-coworker from WelZyn, Isaac Steiner. Steiner brings the two up to speed, explaining how Potolsky's employers, WelZyn--and through ownership--Wayne Enterprises, were producing a serum for super soldiers. Though first named "Venom," the serum underwent many evolutions under Potolsky's guide before Potolsky went rogue. When Gordon and Bullock press Steiner on his involvement with the deadly drug, he reveals that Potolsky planned to exact revenge against the Wayne family by exposing it to a crowd at that night's Wayne charity event--an event that Bruce Wayne begrudgingly attends at Alfred's behest.
At the event, Bruce confronts a Wayne Enterprises employee on the board's involvement with the Arkham Project. Before he can press any further, Potolsky sends a broadcast revealing Wayne Enterprises involvement with the Viper project before pumping the room with Viper gas. As the crowd breaks into a panic, Gordon and Bullock break through the locked doors and evacuate the building.
Gordon and Bullock then find Potolsky on the building's roof, where he inhales an entire vat's worth of Viper. Driven mad by the high dosage, Potolsky doesn't attack Gordon or Bullock at all. Instead, he jumps off the roof with the assumption that he is strong enough to survive to fall. Unfortunately, he is dead wrong, as Bullock remarks, "I guess you can have too much of a good thing." Very droll, Detective.
Hoping to locate more Viper at Potolsky's temporary laboratory, they find that it's scrubbed clean of all remains. Unbeknown to them, Wayne Enterprises carefully are watching their every move. Though they will let Bullock and Gordon's investigation go uninterrupted for now, the Board makes it clear that they will stop the GCPD members if they unearth too much information.
The Penguin's key intel for sabotaging Falcone's casino proves fruitful, bringing him closer into Maroni's inner circle. And that's not the only bad news for The Roman, as Fish and her Russian partner beginn plotting their own takedown of Falcone . That takedown starts with Fish's "secret weapon," the girl she hired to train and act as a lovable foreigner with an attraction to elder mob bosses.
Befriending Falcone in the Gotham City Park, Fish's Weapon plays him an opera song on her mP3 player. As the two listen together, the episode closes on the sound of Carmine's impending doom.