Agent Secret has to retrieve three secret containers before the evil Lady in Pink does. With the help of Miss T. and Undercover Contact Austin, Secret must travel the globe to obtain the containers before the Lady in Pink gets them, and unhatches her "recipe for disaster".
Pablo is seen sitting on the picnic table, holding an apple juice box. He introduces himself as "Agent Secret", a well-respected secet agent. He also tells the viewer he likes his juice boxes shaken. Pablo sings International Super Spy and then heads to Spy Headquarters. But The Lady in Pink, the most evil mastermind in the world, is spying on Secret.
Agent Secret's boss, Miss T., tells him he needs to retrieve three containers. She explains how no one knows what is in the containers. But they are probably extremely dangerous. T. tells Secret how the journey will probably be his most life-risking quest yet. But Secret accepts the job and heads to a pub in London to receive information from his secret contact, Austin.
Meanwhile, inside Big Ben, the biggest clock in London, Lady in Pink is explaining the situation to her henchman. She Cyndi Lauper and Henchman Tyrone begin to sing The Lady in Pink. She heads out to the pub.
Inside the pub, Pablo is waiting to order. Austin approaches his table. Pablo yells "Hey! You're my secret contact!" but Austin quickly covers his mouth. He orders a banana split, and the banana split turns out to be a PDA. Tasha tells him that the first container is hidden inside the glass building. But Lady in Pink, who had been listening the whole time, decides to head out to the glass building.
Secret gets to the glass building first, and uses his hat propeller-laser to get into the building. He realizes that the only way to activate the door containing the first container is to dance on an electronic mat, following the moves on a screen. After Pablo succeeds to retrieve the container, Lady in Pink and Henchman Tyrone -who were waiting outside the building- steal the container. The three sing the first third of Good and Bad Don't Mix. At the end of the song, Pablo regains the container. Before Lady in Pink and Henchman Tyrone can steal back the container, Pablo jumps in his car, which transforms into a helicopter. Pablo then flies into the night while his jingle plays (International...Super Spy!).
They begin a fight trying to grab the container, and Secret runs off into his spy car with it. He turns a knob to turn his car into a plane and zooms off.
He calls Miss T. and learns to go to a restaurant in the snowy mountains. He orders an ice cream sundae and gets information to go to Dare-Dairy Farm to receive the second container. Pink had been overhearing this, and quickly rushes to her snowmobile. They head to Dare-Dairy Farm.
Pink orders Tyrone to stop anyone who tries to get into Dare-Dairy Farm. She heads in. But Secret disguises himself as a tree and walks over to Tyrone. He taps Tyrone on the shoulder, causing him to walk to the other side. Agent Secret rushes into the farm, as Tyrone comes back.
The Lady in Pink had recently noticed the hall was covered in booby traps. She had to escape doors that tried to crush you! After risking her life, and succeeding to get to the end, she dances on the mat. She is interrupted by Agent Secret, who then makes the dance machine activate to multi-dancer mode. They both repeat the moves on the screen until the container comes out of the door. Secret tricks The Lady in Pink into walking away, and Secret steals the container. Lady in Pink quickly notices it was a trick, and tries to grab it from Secret's hands.
Meanwhile, outside the farm, Tyrone wonders about the "tree". The Lady in Pink is running out the door, chasing Agent Secret. Agent Secret rushes into his car, turning it into a snowmobile. The Lady in Pink and Henchman Tyrone also rush to their snowmobile and start chasing him while singing Good and Bad Don't Mix. They steal the container from him, but get hit by a big hill. The container flies into the air, as Secret transforms his snowmobile into a helicopter. He snatches the container and calls T. Miss T. tells him to go to a snow cone parlor in Hawaii.
Pink and Secret go to the snow cone parlor. Secret orders a cherry snow cone, and it turns out to be a hologram of Miss T. He gets information that he has to go to a Tiki Island in order to get the last container.
Secret heads underwater with a seagull disguise on his head as he makes his way to the island. Pink and Tyrone follow him, wearing shark diguises on their heads. All three of them are now dressed in wetsuits. Pablo reaches the island first, and rushes inside the waterfall and finds a secret passageway to the dance center. All three of them dance, but after the instructions Secret changes his voice to match the instructor's voice and tells the others to close their eyes and count to ten. They reach seven, but Lady in Pink yells "SECRET!" instead of eight. Tyrone is questioned and asks "Don't you mean eight?" but quickly realizes that Agent Secret and the Lady in Pink are running off. The Lady in Pink rides away to catch up to Agent Secret.
They begin a fight trying to grab the container, while singing the third and final part of Good and Bad Don't Mix, and Secret runs off into his spy car with it. He turns a knob to turn his car into a plane and zooms off.
Secret now has all the containers, and starts flying to Headquarters. When he gets there, Miss T. isn't in her chair. The Lady in Pink's head appears on the screen announcing he needs to give her the containers. He asks why, but Lady in Pink just points the camera at Miss T., helplessly screaming. She makes a joke, saying "A little hippo told me.". She tells him that if he doesn't come to the clock immediately, 'the hippo gets it'. Secret realizes that she meant that Miss T. will get threatened (tickled) if he doesn't hand over the containers. Austin calls Agent Secret, Agent Secret tells him to "Deliver a pizza" to Big Ben.
He heads to Big Ben. But Lady in Pink tells him that her henchman will slide him the remote to her tickle table that will threaten T. But only if he slides over the containers. He slides them over, but Tyrone refuses to slide over the remote. Uniqua confirms that she did trick Pablo and sings A Recipe for Disaster. The doorbell rings. Austin pops out, wearing a pizza man disguise. He begins to hand Tyrone the pizza, but Pink realizes it is Austin. Tyrone is horrified and nearly breaks out in tears at the fact of not eating any pizza. Lady in Pink opens the first two containers. The first one contains a glass, and the second one contains milk. As she makes ready to open the third, she gets interrupted. It turns out that Secret's tickle table didn't work on Secret because he is not ticklish, and Pink's attempts to make the tickling speed up causes it to short circuit, because of this the lights go out, random noises including a cat scream, ghostly noises, and other scary and hilarious sounds alarm Tyrone as he searches for the light switch. When he turns it on, all three of the spies are gone!
They all run outside when Pink opens the final container, which contains chocolate syrup, but she drops it, and the bottle lands on the hour hand of the giant clock. Making her way back inside, she opens a secret panel on the clock face and slowly makes her way out to the edge of the hour hand trying to get the syrup. As the hand moves, the syrup falls off. Desperate to have her chocolate milk, she jumps off the hand, trying to catch the syrup. As the Lady in Pink tumbles through the air, Pablo asks for the pizza. The pizza is actually a jetpack. Secret catches Pink and the syrup, and activates the parachute. "You saved me!" says Pink, acknowledging Secret's heroism. As they float to the ground, Uniqua tells Pablo that she always wanted to be a super spy, more than anything.
Back inside the Lady in Pink's lair, the friends gather around a table. They pour milk into the glass, when they realize they can't make chocolate milk without a spoon to stir it with! But Secret announces that there is another way to make chocolate milk: shake it. So they all have chocolate milk.
Agent Secret raises a toast to the newest members of International Super Spy Headquarters: Agent Pink, and Agent Tyrone. Together, the five friends sing a reprise of International Super Spy and the Lady in Pink sings that she's glad to be a 'good guy'.
After the song, Pablo invites them all over to his house for more chocolate milk at his house. They enter his house. Pablo opens the previously closed door and shouts "Shaken!".
International Super Spy was a Nickelodeon movie success. It was a commercial hit and was watched by 100,000,000 viewers worldwide on its original airdate. The film was not a major Nick film, but was classified a Nickelodeon Movies production. The Super Secret Super Spy DVD was bought by over 100,000,000 customers around the globe.