The story follows a light-bulb-head orphan, named Otto Osworth, who is under the watchful eye of the nasty nun of the School for Wayward Tots, named Sister Thornly, who treats him badly for reading history books. Otto soon finds his ticket out of the orphanage, by using his knowledge of history to talk time cop Buck Tuddrussel and his robot Larry into abducting him. He is suddenly zapped to the satellite and to Eli Whitney's time where they must convince him to invent the cotton gin, not the flesh-eating robot.

Tuddrussel is showing Otto some outrageous souvenirs from the past when they get a mission to the time of the Trojan War, where the Greeks sneaked a giant, wooden horse into Troy's kingdom, filling it with solders to attack when the horse is opened, to win the war. Instead, they're filling it with candy for the king of Troy's birthday!

Confucius was famous for coming up with short phrases. "Short phrases?" any one of the three Time Squad members might say. "You've got to be kidding!" And it's true! He's making his stories way too long! But will Tuddrussel's beating him up help?

The Time Squad must go back to the year 1899 to convince Sigmund Freud to stop hypnotizing his patients and making them act like animals (done by someone else).

Then, they meet up with famous artist and sculptor Leonardo Da Vinci. They have to find some way to encourage him to create great art.

After a problem with Tuddrussel messing with the controls, Time Squad travels to the year 46 BC to improve upon the flimsy city of Rome for Julius Caesar. But by the time the mission's complete, Tuddrussel doesn't want to leave! The Romans don't want him to leave ether. And Larry is forced by program to stay! It's up to Otto to train out-of-shape Caesar to beat Tuddrussel in combat to get everyone to snap out of their foolishness.

After chaos from Otto and Tuddrussel in the gulf dome, Time Squad visits Robin Hood, who is stealing from the poor and giving to the rich, instead of the vice versa action he's supposed to do!

"Honest Abe" Lincoln grows tired of being upstanding when he starts getting ridiculed for it. When he finally snaps and becomes the prank-pulling "Dishonest Abe", it's up to Time Squad to give him a taste of his own medicine.

Time Squad goes back to the Age of Pirates, where Edward Teach (AKA Blackbeard) is more concerned about saving the environment than looting and pillaging, much to the chagrin of his crew.

During a musical argument between Larry and Tuddrussel, Time Squad gets sent to the time of the great musician Ludwig van Beethoven. Now they have to get the message across to him, "No more pro wrestling!"

After being upset with grumpy Tuddrussel, Larry is delighted to discover that instead of dumping tea into the Boston Harbor, the Sons of Liberty are having civilized tea parties. Tuddrussel and Otto have to convince them into dumping the overtaxed colonial beverage, for the sake of all America!

As an aftermath to Larry showing Otto their awful bloopers from their missions before he came, Time Squad is now trying to get the Wright brothers to making the first airplane instead of working on their incredibly dull stunt show, and Otto is scared when Tuddrussel wants to do things his way.

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After convincing Copernicus to be an astronomer, not a farmer, Time Squad finds out that Larry's time circuits have to reboot and they're stuck in the past for a few minutes. But it seems like a few hours, as they try to come up with things to look at to "kill time" as they wait for Larry's time circuits to warm up!

Time Squad goes to 1945 to prove that Albert Einstein is a math genius and not a car salesman.

Larry refuses Tuddrussel's orders and accidentally downgrades himself. Tuddrussel asks for a burger, so Larry gives him burgers everywhere he goes.

Edgar Allen Poe, the writer of horror stores is writing cheerful stories! Can Time Squad remind him how horrible the world can be?

While checking on the subjects of their past missions, Time Squad gets sent on another colonial mission for Betsy Ross, the designer of the first American flag. Now they have to convince her to shut down her Woodstock-1969-ish camp and return General Washington's troops to him (Yes, and to make a flag for them too).

Winston Churchill, the prime minister who leads England through World War II, is also leading everyone into being naked! Including Larry!

It's the time of George Washington Carver, the man who invents more than 100 uses for the peanut. When Time Squad gets there he's doing just that. "Where's the glitch?" Larry wonders. The glitch is that George's brother, who hates the peanut, is trying to make it look bad!

Kubla Khan, a conqueror as a child, when history unravels, is a comic book collector. When Tuddrussel tries to bring him back by ripping one of his comics, Otto and Larry must help him escape before he's executed!

Their mission: Lewis and Clark, the two men who explored most of future western America. But the partners have broken up and Time Squad will have to do whatever it takes to bring them back together.

After a mission to Ivan the Terrible, the Russian king, he and Tuddrussel worry about them missing each other. Thus, he sneaks Ivan onto the satellite. But how long will it be before Otto and Larry discover him because of all the doggy clues Ivan's leaving?

Buffalo Bill was the one to start the first mail service called the pony express. But when Time Squad finds him, he has some crazy ideas on his mind other than postal service. And I mean crazy. Time Squad must get him on his horse, delivering mail.

Cleopatra decides to convert King Tut's pyramid into a mall.

The Earl of Sandwich gives his new food the wrong name.

When Tuddrussel squashes a fly in the Stone Age; giant flies are ready to squash them in the Time Travel Age! They must go back in time to stop Tuddrussel from ever squashing the fly!

Sitting Bull was known for battling Colonel George Armstrong Custer after seeing a sign from his ancestors. But instead he thinks they're telling him to "get down" as some people may say it.

Oh NO!! Mean ol' historically incorrect George Washington's on the satellite!! He's set it toward the earth and on fire!!! Right after he leaves, the satellite crashes into the earth, and Time Squad has lost their lives!!! In a virtual reality game, that is. Right after, they are sent on a mission to Harry Houdini who is using his escape tricks to rob places.

After Larry stands up to Tuddrussel thanks to a program called "Bustin' the Barrier" by Thor Robertson, the two neighbors who always fought, the McCoy's and the Hatfield's, get a visit. But the McCoy's aren't sticking up for them. With a little help from Larry's special program, the two families start to--get along?! Tuddrussel and Otto must get them fighting, for the sake of the mission.