This is the first mission of Flint, Sarah and Tony as time detectives. The team are sent back to the 2nd century A.D. Japan to retrieve and rescue the Time Shifter Jitterbug. On arrival, the group help Queen Himiko of Yamatai and her sister Nashimi to restore order after Petra Fina and her gang overthrew them and took them as prisoners.

The team heads back to 16th century South America in order to rescue the Time Shifter Eldora. Upon arriving, they are captured by Spanish Conquistadors and end up as prisoners where they try to extract the location of the Golden Condor from them. In help of the leader's only son named Lucas, they escape and aim to help a group of ancient Incas to return to their village and to prevent further attacks from the Conquistador who are revealed to be acting under Petra Fina's orders.

The team is sent back to the Heian Period of Japan (794 A.D.) in search of the Time Shifter Talen. After confronting the villains, Petra Fina and Flint are dragged into the tale of Princess Kaguya as Talen attempts to escape. Within the story, Flint befriends Talen (who disguises herself as the titular Princess Kaguya) and all three eventually escape the story. Petra Fina subsequently captures Talen and Flint must fight to rescue his new friend.

The team is sent back to Russia in 1812 to search for the Time Shifter Mosbee. There they encounter the invading forces of the First French Empire under Napoleon Bonaparte, as well as Mosbee who ends up being brainwashed by Petra Fina. Petra Fina secures the loyalty of Napoleon and his forces after using Mosbee-Con to freeze their Russian opponents. Flint must fight Mosbee-Con and restore order. A mysterious character also makes a first appearance to help Flint. Upon Mosbee being free, Napoleon decides that Russia is too cold to invade and has his forces retreat back to France.

The team goes back to the year 1492 to look for the Time Shifter Coconaut, where they find themselves pressed into service for the famous explorer Christopher Columbus upon being fished out of the ocean by his crew. Coconaut is revealed to be assisting Columbus in his navigation. Petra Fina uses this fact to inspire distrust for Columbus amongst the crew and also to steal Coconaut and take command of the fleet where she plans to rename America as Petra-Merica. After escaping from abandonment on a desert island, Flint and his friends rush to set things straight and free Coconaut.

Travelling back to Japan in 1582 (during the Azuchi-Momoyama Period) in search of the Time Shifter Bubblegum, the team arrives at Azuchi Castle, where they find Bubblegum in the companionship of Oda Nobunaga and his attendant Mori Ranmaru (who is portrayed as being female in the series). When Petra Fina and her gang attack the castle and brainwash Bubblegum, the heroes and Nobunaga are subdued in battle, only to be rescued by Ranmaru and Coconaut-Master. Together the group fights Bubblegum-Con to thwart Petra Fina's plan.

The team is sent back to Ancient Egypt (323 B.C.) to search for the Time Shifter Lynx. On arriving, the group find Lynx under the command of Petra Fina who styles herself as a Queen. When Flint is brainwashed by Lynx, Tony and Sarah engage Lynx in a game of riddles and beat him by using the Riddle of the Sphinx, breaking Petra Fina's spell. With the aid of Bubblegum-Master, Flint confronts Lynx-Con.

The team is sent back to mid 19th century Paris in France to search for the Time Shifter Artie. At the same time, Petra Fina receives a portrait of the Dark Lord. On arriving they find Artie in the company of a young Auguste Rodin, who has been using Artie's powers to animate his drawings. When Petra Fina and her gang arrive and brainwash Artie, Flint (with the peculiar "help" of Lynx) takes on Artie-Con.

Plotting to capture Getalong from the Time Detectives and use her power to be married to the Dark Lord, Petra Fina and her henchman set up a trap for Flint, Sarah and Tony in Baghdad in the year 1539, misleading them into searching for a Time Shifter. There they are caught, but end up engaging in battle with the cat form of Petra Fina's Catamaran, which is defeated with the help of Getalong.

The time detective team travelled back in the year 1956, where they encounter the Time Shifter Batterball and the young, rude, and cunning baseball player name Babe Ruth wherein he always uses Batterball for his prank plan on his bullies much to Tony's disappointment and confronts him to challenge to a real baseball game together with the troublemakers (which is Petra Fina and his henchmen).

The Time Detectives had to go back to 15th century in Transylvania to retrieve another Time Shifter named "Bindi" which she is in the possession of Count Vlad Dracula or just simply Count Dracula which his fellow people in his villagers believed that he is actually a vampire. Upon meeting with Vlad Dracula, the mysterious guy who helped Sara in some episodes, revealed his identity as Merlock Holmes of the Time Bureau and assigned as undercover detective to observe Flint Hammerhead in his missions. In the end of this episode, Bindi choose to side with Merlock because of her faith to him and also because Flint already sees that she wants to go with Merlock rather than their team.

This is the only episode that Flint and the team travelled back in time not just one, but two. It started on Christmas Day where they will also meet a lonely young girl named Maria in ancient France in hopes of finding her missing mother and that is with the help of her own-believed angel which is the Time Shifter named Elfin (which he has an ability to turn anything into a toy). As Flint works to prevent the death of Maria's mother, they also must deal with Petra Fina even when she transforms Elfin to Elfin-Con. They defeat him with the help of Batterball-Master. Afterwards, Jillian Grey stated that tampering with history is illegal. Though she will overlook it.

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The time detectives had to go back in the year 2000, where they have to find the group of Time Shifters named The Cardians. But upon reaching the timeline, Sara and Tony surprised that the time they've gone to is the time when their uncle Dr. Goodman is a teenager and likes to smoke a lot and that explains why he doesn't have a girlfriend up to now. While witnessing the heroic deeds of the Cardians, Flint also must deal with Petra Fina when she takes control of the Cardians. After being freed by Flint, the Cardians form Cardian-Master to fight with the cat form of Petra Fina's Catamaran.

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After Bindi runs away from Merlock upon being neglected, Petra Fina captures Bindi and manages to get Bindi under her control. Now Merlock and Flint must rescue Bindi from Petra Fina's control.

Upon arriving on what will be Easter Island, Flint's group finds the Time Shifter Moah helping the native children. When Petra Fina arrives and Flint fights off her attempts to Petra Stamp Moah, Petra Fina has Dino and Mite fire the Petra Stamp Missile which turns Moah into Moah-Con where he causes a volcanic eruption enough for Mosbee to be called in. After Moah is freed and Petra Fina is defeated, a tidal wave threatens the island which leads to Moah becoming Moah-Master where he jumps down on the ground enough to bring up the Moai that intercept the tidal wave.

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Ms. Iknow has been making her students due many laps during gym class until Pterry arrives telling Flint that a Time Shifter has been sighted in Ancient Greece within the year 4 BC. Ms. Iknow uses this cover to leave and change into Petra Fina while Flint's group heads to 4 BC. Upon arrival, they find the Time Shifter Muscle helping a struggling athlete named Damon.

It's Sunday, the Goodman residence had a general clean up for their homes, all of the Time Shifters helped them (except Moah which he is really big). Petra-Fina in the form of Ms. Iknow plans to capture the time shifters from Dr. Goodman's possession in order to give all of them to Dark Lord, by using or dating Flint's dad Rocky Hammerhead. After Flint and his friends realized that his dad is gone, they had to go to the city to go and look for him. Meanwhile, Merlock and Bindi sees Rocky that he is dating with Ms. Iknow, so he had to tell to Sara that Rocky and Ms. IKnow are dating only and they have to watch them secretly to find out if Ms. Iknow has feelings to Flint's dad or just using him as her guinea pig.

Flint, Sarah, and Tony arrive in the Grand Canyon when pursuing the time-traveling Time Shifter Unita-Master. A fight between Flint and Petra Fina's group lands them in the Land of Time where Flint has his first encounter with the Old Timer and how the Time Shifters were scattered throughout time by the Dark Lord during an earlier attack on the Land of Time.

After being lost in time following the incident in the last episode, Petra Fina, Dino, and Mite are apprehended by the Time Police. When Petra Fina, Dino, and Mite make an escape during interrogation, Dino and Mite capture Dr. Goodman as Petra Fina receives an assignment from Dark Lord to search for the Time Shifter Raldo. The time period that Raldo is in happens to be Petra Fina's childhood.

Flint's group arrives in the Medieval Ages where they meet the child form of King Arthur who has befriended the Time Shifter Leafy. Because of Arthur's cowardice, Petra Fina manages to get control of Leafy.

During a mission to get the Time Shifter Monk, they find him in the company of Saito Musashibo Benkei where they steal Rocky from Flint. While working to get his father back from Monk and Benkei, Flint must also contend with Petra Fina when she takes control of Monk.