Doris the dolphin's quest to rescue her brother Francis from Seaville brings her to the lovestruck Kowalski.
After testing out and falling out of his anti-gravity socks, Kowalski is approached by a platypus named Parker, who asks that he come with him. Kowalski asks for a reason and Parker says he needs to say one word. The next scene shows Kowalski grabbing a myriad of items from his lab and leaves in a hurry. Curious, Skipper unveils a monitoring station on their HQ's multi-purpose door (which is the same door to Kowalski's lab) to check the surveillance tapes. After accidentally showing footage of Private doing an impression of Skipper and Rico drinking spoiled milk, they find the footage of Parker and Kowalski, revealing that the platypus said, "Doris", Kowalski's dolphin crush. Skipper declares this to be trouble; Private, slow on the uptake, realizes that Skipper has been spying on them all.
At the docks, Kowalski assumes that Doris had finally come to her senses and would accept him. Upon seeing her, he is lovestruck and babbling incoherently. After calming down at Doris' instruction, Kowalski is heartbroken to hear that Parker is her latest fling.
Meanwhile, the other penguins race to catch up with Kowalski. Skipper explains that they need to "talk and/or pound some sense into Kowalski's thick head!" Private asks how bad Doris can be. Skipper says that the last time Doris rejected Kowalski, he refused to leave his bunk for six months; he adds that "cleanup duty" was not pleasant.
Kowalski freaks out and throws a tantrum, claiming that Parker is not good enough for Doris. The sweet dolphin points out that he's had complaints about her other boyfriends and insists that she only wants to be friends with him. The rest of the team arrive in time and prevent Kowalski from having yet another emotional breakdown. Skipper authorizes and encourages use of excessive force. Rico enthusiastically regurgitates a lead pipe but Kowalski tackles him, saying it's not necessary. He attempts to walk away to mope in his own misery, Parker stops him, saying that Doris didn't summon him just to rip his heart out (again). Doris reveals that she's been trying to rescue her brother from a water park known as Seaville. With renewed hope, Kowalski plans to rescue her brother to hopefully woo her back to him and away from Parker.
After being forced to work with Parker, who seems to outdo Kowalski in nearly everything, they finally manage to grant the entire group access to the park.
A short search brings them to Doris's brother's tank, upon which she calls for a dolphin named "Francis". Francis is revealed to be none other than Dr. Blowhole. However, the mad dolphin genius remembers none of them, not even his own sister. After the last Mind-Jacker incident, he's fully convinced he's Seaville's 2nd most popular performer, "Flippy".
Stunned, the penguins can't believe this turn of events and Doris is confused as to why they're calling her brother, "Dr. Blowhole". She only remembers the innocent, happy-go-lucky Francis.
Parker reveals the truth to them that Flippy, Francis, and Dr. Blowhole are one and the same dolphin. The platypus further shocks the group stating that he knows because he works for Dr. Blowhole and only came to collect his pay which he is due.
Parker then attacks the entire group and brings "Flippy" back to Blowhole's secret island lair. He asks the lobster minions for his pay but they admit that only Blowhole can pay him. They attempt to "de-jack" Blowhole but his segway doesn't contain the Mind-Jacker.
Back in Seaville, Kowalski gloats to Doris that he was right all along about Parker. She points out that he's been suspicious of all her boyfriends. She and the penguins escape Seaville to follow "Flippy" and Parker. During their escape, Manfredi and Johnson are seen in an enclosure. They call for their leader, but they are not heard. The four penguins declare that they shall never return to Seaville and swim off.
Back at Blowhole's lair, the lobsters attempt to jog their master's memory back by showing him slides of the Chrome Claw, Project Bad Tidings and their three-day weekend in Cancun to no avail. An impatient Parker demands his money. Shortly, the penguins and Doris arrive at the lair and a battle ensues. Kowalski takes on Parker and Skipper, believing Blowhole to have regained his memory, tackles him. "Flippy" is confused as to why Skipper attacked him and why everyone calls him "Blowhole". Skipper realizes that his mind hadn't been "de-jacked" yet.
Doris watches on, but wants to help out in the fight. She soon finds the spare segway and tries to drive it inadvertently making the situation worse. The segway is out of control firing lasers at everyone, but Doris then accidentally activates the Mind Jacker.
Skipper tries to get "Flippy" out of the blast's range so he won't regain his memories, but the military penguin is blasted by the Mind Jacker.
Parker, after fending off Kowalski, attacks Doris then takes control of the Mind Jacker and restores Blowhole's memory. The evil dolphin is back once more, so now Parker can get paid.
The callous platypus demands his pay which Blowhole assures him he'll get once the penguins are destroyed. Doris is finally aware of her brother's true self and is very disheartened by it. Blowhole traps his sister in a tank to keep her from interfering. (He doesn't harm her which shows he does care for Doris.)
The now restored Dr. Blowhole fulfills the plan which he left off on: Project Bad Tidings. With a tractor beam, he plans to bring the Moon closer to the Earth which will cause worldwide flooding. Once the flooding is complete, he'll be ruler of a waterlogged world with humanity destroyed.
Kowalski knows the plan will work, but decides to play mind games with Blowhole to stall him. As Blowhole leaned in closer, Kowalski hits him with his tongue, knocking him off his segway and hit the button to free his friends. They then imprison Blowhole in Doris' tank before Kowalski gloats that his plan would work. Blowhole then orders the lobsters to fire the cannon but Rico knocks it over with dynamite. The cannon then starts attracting to it anything not bolted to the floor and the lobsters can't shut it off with the power switch destroyed. The penguins attempt to escape before the cannon explodes, only to spot Parker attempting to steal their submarine. Doris hops onto the segway and knocks Parker off, before breaking up with him. They escape the imploding volcano base.
The group returns safely to New York. Kowalski and Doris finally kiss and make up. The scientist couldn't be happier with the outcome.
Private asks Skipper if they've seen the last of Blowhole. He says that his arch-nemesis would likely be rebuilding his criminal empire.
Meanwhile, floating on a wooden plank, Blowhole and Parker survive the explosion. Parker still demands his pay from Blowhole, but the dolphin admits his checkbook was lost in the wreckage. Not satisfied with that answer, Parker points Blowhole. The mad dolphin then offers some gift cards that he has as a substitution as he paddles the wooden plank away.
- He's Doctor Blowhole (played as the theme song)