The episode begins with a shadowy figure that looks like Plankton opening a safe that has the Krabby Patty formula in it. SpongeBob turns the light switch on, and then it reveals it was just Mr. Krabs checking to make sure that the secret recipe is still safe and that Plankton did not try to steal it yet. He has not tried to steal it in a month, so he must be planning something big which is what Mr. Krabs is thinking. Squidward had just then entered the office and said, "Hello." When Mr. Krabs said one of his employees will have extra work, Squidward said "Good Bye," and left, leaving SpongeBob to do the work as being a spy to follow Plankton to see what he is up to (in this scene, SpongeBob makes a parody of the gun barrel sequence, from Patrick's straw). Then Patrick hollered that he also wanted to become a spy. Mr. Krabs gave them a Patty that will tell them that their assignment is to follow Plankton to see what his plans are. If they fail to get gadgets, and do not accept the task, they will be fired.
SpongeBob and Patrick visit Sandy's Treedome to ask her about spying, and Sandy shows them spy inventions. SpongeBob was excited to use the equipment, but Sandy refused to let them use any of them, as she felt they would just mess it up and then Patrick uses the knockout gun to knock Sandy out and they stole the equipment. One of the gadgets that they steal is the laser-equipped Bermuda shorts. Patrick replaces his normal pants with these. He wires the pants to his butt, so that it will fire lasers whenever he farts.
They started following Plankton, and it is revealed that Plankton buys baby clothes and has to buy stamps for mail. They tell Mr. Krabs everything and Mr. Krabs writes these on a chalkboard.
Later that night, SpongeBob and Patrick are on the rooftop of the Chum Bucket trying to get inside. Patrick lets out a large fart causing the laser pants to make a hole for them. Plankton thought that they came in late at night to eat his food while Mr. Krabs was not around. Patrick tells SpongeBob that he REALLY has to go to the bathroom and he cannot hold it in. Patrick also says that his laser pants are not working right. Without his control, Patrick farts causing the table behind him to disintegrate. As he keeps on trying to hold it in, Patrick's butt begins to shake because of the gas inside him. Plankton tries to offer a raspberry ice tea or a bran muffin, even a prune danish to Patrick, unaware that he has to use the toilet. Patrick tells SpongeBob that he has to go NOW. When the gas pressure becomes to much for him, Patrick begins to fart uncontrollably. As SpongeBob, Patrick, and Plankton scream, the lasers shoot out of the laser pants making holes in the walls thus destroying the Chum Bucket.
Angry, Plankton sends a giant blimp to the Krusty Krab. Mr. Krabs thought that night had come early, but Squidward points to Plankton's blimp. When Mr. Krabs tells everyone to get into their positions, Squidward runs into the men's bathroom. Plankton pushes a button that starts playing annoying music that makes the customers leave. Mr. Krabs says that if he wants his customers, he can have them. He sucked them into a giant cannon, and shot them at the blimp using the customers and, unfortunately, Squidward. Unluckily, the attempt failed, as the customers always bounced off the blimp. SpongeBob tells Patrick that it is all up to them to save the Krusty Krab, but Patrick jumps off the blimp and accidentally lands in the cannon, which fires him right at the blimp, causing it to burst. The Krusty Krab blows up as well.
Plankton, now having the secret formula in hand, laughs and states "I WIN! I ALWAYS WIN!," but SpongeBob reminds him that he always loses. Plankton corrects SpongeBob that he always wins and reveals that it was Mr. Krabs in disguise. The other Mr. Krabs was actually a robot controlled by Plankton. Mr. Krabs and Plankton did a bet that if Mr. Krabs disguised himself as Plankton so he can steal the Krabby Patty formula better than him and if the Chum Bucket gets destroyed, Plankton would pay him a dollar. After Plankton gives money as part of the bet, Patrick yells at them to stop and rips his skin off showing that he is Squidward. SpongeBob asks that "if he is Squidward, then who is the other guy?"
Just as SpongeBob tries to pull off the other guy's mask, Squidward was trying to tell SpongeBob that he was not wearing a disguise and that he was the real Squidward. He takes his ripped face back, they then continue to take off disguises, and Sandy shows up and says that it is the wrong disguise, then SpongeBob appears. SpongeBob takes off his disguise and Patrick appears. Then both of them return to their real selves, then SpongeBob tells Mr. Krabs that he is confused that there are two Patricks, and they both started laughing. After the two Patricks stop laughing, it cuts to black, ending the spy episode.
Shower In A Can!
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Originally, instead of Plankton finding SpongeBob and Patrick, when they fall into the Chum Bucket, SpongeBob and Patrick were going to find a domestic dispute between Plankton and Karen, which featured Plankton not wanting to go to Karen's Mother-in-law's house because she was going to be a car alarm that was going have only said, "Stay away from the vehicle."  It should be noted that "Karen's Mother-in-law" may have been a mistake and that the commentator was referring to Karen's Mother, whom would later become, "E.M.I.L.P.". However, this has not been confirmed.
When SpongeBob is seen walking inside the dot (when Patrick was looking through the straw), it is a parody of every James Bond movie before this episode.
In this episode, SpongeBob walks into the dot onscreen and spins around with his spatula in hand.
In the movies, Bond walks into the dot (which is a gun-barrel pointed at him), spins around and shoots the screen.
The bet between Krabs and Plankton, using their "usual wager" of one dollar, is a reference to the main antagonists of Trading Places.
"The Krusty Krab" sign has black writing and is a bit darker.
On the DVD release, if one plays it frame by frame, they can see closely in the explosion cloud that the Krusty Krab is not actually being destroyed. When the explosion cloud disappears, the Krusty Krab is instantly destroyed.
After SpongeBob and Patrick fell on the sidewalk, SpongeBob was lucky to save his skin when his face was mixed up.
Patrick's body was scalded from the sidewalk falling.
When SpongeBob and Patrick were about to enter into a spymobile, SpongeBob runs to his right while Patrick runs to his left.
As they enter into the vehicle, Patrick somehow runs back to the right.
If one looks closely, when Patrick blows up, when he speaks his feet are skeletal, but when he pulls his pants up they are normal.
After Patrick destroyed the Chum Bucket with lasers, it was night.
When they were lying on the ground after that, it was daytime.
After Patrick cuts off a rectangular hole on Chum Bucket's roof, the excess roof is missing on the bird's eye view when SpongeBob enters.