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. Squidward had just entered the office said, "Hello", and 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's 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 don't accept the task, they will be fired.
SpongeBob and Patrick go to Sandy's tree dome to ask her about spying, and Sandy shows them spy equipment. 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 steel is the Laser pants. Patrick replaces his normal pants with these. Patrick 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 but 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 absent. Patrick tells SpongeBob that he REALLY has to go to the bathroom and he can't hold it in. Patrick also says that his laser pants aren't 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 bran-muffin and a prune to Patrick, not realizing that he has to use the toilet. Patrick tells Spongebob that he has to go NOW. Because of the pressure, his gas bubble finally bursts and he lets out a barrage of farts. 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 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's all up to them to save the Krusty Krab, but Patrick jumps off the blimp and accidental lands in the cannon, which fires him right at the blimp, causing it to pop. The restaurant 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's 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 wasn't 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's 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.
The episode title was going to be called "SpyBob" but later it was changed to "Spy Buddies".
Dish Network and Time Warner Cable still refer to this episode as SpyBob.
The Nickelodeon schedule calls this episode SpyBob.
The password to the Krusty Krab was: 2684
The combination to the safe was: 30-5-20-0
In the beginning of the episode, it appears that Plankton knows the code to the Krusty Krab and the vault combination, but then it turns out to be Mr. Krabs. However, In the end of the episode, Plankton turns out to be Mr. Krabs in disguise and Mr. Krabs is revealed to be robot Krabs being controlled by Plankton. This means that Plankton actually does know the code and vault combination, it seems that he only knows them in this episode.
The Secret Formula: (x-2)+1=Krabby Patty as seen on the page of the secret formula after "Plankton" says "I always win."
Running Gag: SpongeBob and Patrick screaming about their spy identities.
You can see SpongeBob and Patrick's spy boatmobile that is a parody of Batman's Batmobile in this episode.
The song used for the title card is used for Action League NOW! for the credits.
One of the scenes from this episode is where when SpongeBob and Patrick are walking behind Plankton, Plankton yells at them in high-pitched gibberish and the two have no idea what he's saying, but in earlier episodes, SpongeBob and Patrick can understand what Plankton says to them.
Unless the laser pants were wired to Patrick's behind, there's no way they'd make him have to go to the bathroom, and there's no way his flatulence would have caused them to fire.
Mr. Krabs and Plankton can both mimic each other's voices.
After Plankton (Mr. Krabs) lifts up the blimp, the foundation of the Chum Bucket is much bigger than normal. That also reveals that there is another floor of the Chum Bucket.
This episode presumably takes place after "Karate Star" due to Patrick having a clone, just like at the end of "Karate Star."
In Poland, this episode is called "Sponge Bond". It's most likely trying reference James Bond.
When SpongeBob is seen walking inside the dot (when Patrick was looking through the straw), it is a parody of James Bond. SpongeBob walks into the dot onscreen and spins around with his spatula in hand. In James Bond, Bond walks into the dot (which is a gun-barrel pointed at him), spins around and shoots the screen.
The Krabby Patty with the taped message on it, and self-destructing, is a parody of the TV series Mission Impossible.
if you play it frame by frame you can see in the cloud that the Krusty Krab isn't destroyed.
If you look closely, when Patrick blows up, when he speaks his feet are skeletal, but when he pulls his pants up they're normal.
When Mr. Krabs is opening the safe, it is night. But when Patrick screams "I WANNA BE A SPY TOO!!", it is day.
After Patrick destroyed the Chum Bucket with lasers, it was night. But when they were lying on the ground after that, it was daytime.
The Guppies 'R' Us store's name is an error because guppies are a type of fish not a baby fish.
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.
The crash of the excess roof is not heard.
In this episode, Mr. Krabs claims that Plankton has been trying to steal the formula for 20 years; however, in "Plankton's Army", he claimed that Plankton has been trying to steal it for 25 years. It's possible this episode took place before "Plankton's Army", which aired three years earlier.