Zack wanted to stay and work on his project with Spencer and Cam, so he tried to trick Floyd, by turning the clock handles back to a certain time but they were transported into the past where they meet a boy. When they returned to their own time, the boy from the past came with them. So now, Zack, Spencer, and Cam has to return the kid back to his time before it's too late.

Zack has a record of the lowest mark at Horace Hyde White, producing an F-minus on a physics quiz, so when Spencer downloaded an internet physics tutorial to help Zack's intelligence, Zack's headphones were plugged into the modem, making Zack a genius. Spencer's goal was to win the Physics competition, but when Zack came in, he was even better than Spence at Science. This almost led to a break up of friendship.

When Zack, Cam, and Spence join to figure out more digits after the decimal for pi, they surf the net to check out information about a new rock star. But when Ms. Arlington arrives, and checks what they were doing, Zack lost himself in the bracelet on Arlington's wrist. Then he could not lie and told everything what the boys were doing, and telling the truth to everyone. Cam and Spence must get him back to normal before blabbers out information that would get them into more trouble.

Gwendolyn is hosting a party and she needs a DJ, so Vernon and Zack tries out. While Zack was trying to practise on his (terrible) DJ skills, he spun a record backwards, and hears something, a message. Spencer was there to stop him, but he did not stop the transfer of DNA to Zack that made him a ""Cool Dude"" Beatnik from the 1960's. During the tryouts, the people did miserably. But when Zack came on the scene, he made a dazzling performance and impressed Gwen, so she let him become the DJ. When Spence and Cam experiments on Zack and tries to reverse the process, Zack plays the record backwards again. Unfortunately, it did not work and Vernon became another copy of what Zack was. Now they have two people who are groovy.

When Zack and his friends go on a camping trip, Zack's father decides to join them to give them tips. Zack, trying to get away from his father wanders into the woods with Spence and Cam. But they were suddenly zapped into another world, and they must try to find a way out.

When Spencer was doing an experiment on Zack for his sleeping habits for the science fair, Spence discovers that Zack can enter other people's dreams. Zack fell asleep after Vernon did, so Zack invaded Vernon's dream. The case is that Zack invade other people's dreams when both are sleeping near each other, and as a result, Zack does not sleep well. Zack enters Gwen's dream for Spencer's experiment for the Science Fair and to get tickets for the concert for Cam, Gwen thinks that Zack is ""the man of her dreams"" so the 3 kids have to finds away to help with Zack's problem of lack of sleep.

Zack creates a comic book about his ears, because he did not like everyone saying that he had big ears. It turns out that Zack destroys the comic and everyone thinks that it was about Zack and Sarah, so Vernon goes to repair it and humiliated Zack by presenting in front of a large audience.

While Zack along with his classmates, visited the museum for a school trip, Zack touched a field phone which gave him shell shock, just like a soldier who had also used a phone in World War I. Now, whenever Zack is exposed to an old object, his personality transforms into the owner of the object. Spencer and Cam must find a way to reverse the effect before Zack touches an object that did not have an owner or existed before the Holocene Period, where humans were not alive yet.

When Daniel Greenburg accidentally buys Girl Power deodorant for Zack while shopping, and Zack uses it, he becomes a girl! Now, Vernon is flirting with Zack, while Gwen starts plucking his eyebrows. And even worse for Zack, Cam is going on a date with Sarah. Zack decides to find out how to change back into a boy after he gets some secret information from Gwen and Sarah.

When Zack's soccer team, coached by Daniel Greenburg who is more interested exercise and fun than winning games, they started to lose too many games. This made Red MacDonald, who coached the Horace Hyde team in the past, angry and possesses Zack's father to coach the team, so they go back to a winning streak to get ready for the playoffs. The Scottish man, wearing a kilt, made the team practise so much until they all start to play really well. When Zack was getting in the way of Red, he turns Zack into a soccer ball. Spencer must try to find a way to get Red out of Dan's body and release Zack from his soccer ball form. Zack decided to make sure their team loses a game to destroy Red, which means they must lose the change of getting into the playoffs.

One minute Cam is making fun of Zack, the next minute he is a frog! Spence and Zack must turn Cam back into a human before Vernon takes his place on the swim team.

A boy named Gilbert, has come back to finish unfinished business when he was alive. And now, Zack is the only one who can see him, so Zack is being blamed for all the pranks Gilbert is setting up. Pranks are pulled all over Zack's house and the entire school. Zack, Spencer, and Cam must find out what Gilbert wants before he gets Zack expelled, kicked out by his father, or being killed.

Zack develops super-human strength to save his father's life. But instead of going back to normal after his adrenaline cools down, Zack gets stronger. So strong he's dangerous!

Daniel Greenburg hates Zack making messes, and he wants Zack to take responsibility and clean up before he does anything else. When Spencer and Cam visits, Zack says he lost his dad's medallion. Cam checks the vacuum, but he turned on the vacuum, and Spencer and Zack are sucked into the Vacuum into the vacuum bag. Cam must find a way for Spencer and Zack to get out of the bag, but it is dangerous for them to just cross through the opening at the top of the bag because there might be a vortex/wormhole that will transfer Spencer and Zack to another dimension. Dan sends Cam out of his house and takes the bag from Cam. So Cam must find a way to get back the bag and release Zack and Spence before they are eaten by a Spider, with the help of Gwen.

Sarah ends her relationship with Zack. Zack discovers a sword in a stone, and pulls it out. Then Merlin appears, who is usually ""an old guy with the blue hat"", is now in the form of a teenager, and reveals that he was trapped in the stone and continued to grow younger instead of older. No one can see Merlin, except for Zack, and no one else could pull out the sword out of the stone except for Zack. Zack decides to ask for getting back together with Sarah, so Merlin grants him his wish if he completes his quest of bravery while Spencer is thrown all around while trying to obtain some evidence of the 2000-year-old wizard.

When Zack decided to visit the Music store to purchase a copy of a CD that would impress Sarah, but Cam was there and suggesting too many CDs. Zack was only able to buy one or two, but Cam kept on stuffing CDs into his hands, and when there was no more places to add more, Cam decided to stuff them into Zack's pockets. When Zack purchased one of the CDs and was ready to leave, the alarm went off, Zack glowed, and Cam told him about the CD that he put in his pockets. Zack was caught and the security guard told his dad that he would not be charge because it was a first offence, but Zack could never return to the store or he will be punished. Zack discovered that he was a magnet for lost things because he found other people's possessions that have been lost. When Zack collects a book by Archimedes, Spencer must find a way to return to Prague in the Czech Republic. Spence e-mailed and sent forms to find out how to send it back, and a man, who said was a book collector, claimed to own th

Zack started joining almost every club at Horace Hyde, and he becomes overworked when he had to attend every club and finish all his projects. When a new mirror enters the school, he discovered that another Zack had entered their dimension from the mirror. Zack Two worked on the projects for all the clubs, while Zack One did the leftovers. Zack Two began signing Zack up for even more clubs, and Spencer and Cam had to try and send Zack Two back, before Zack One had so many things on his schedule that he would kill himself.

Zack's mother returns to Zack and his father so she could spend some time with Zack. Zack gets in the middle of arguments of who would keep Zack, because his father wanted Zack to spend time with him to watch games while eating dinner, while his mother wanted to talk to him during dinner and see what has been happening in his life. When Zack drinks an Orange Fizzy Pop, he had the ability to transport from different locations, which interested Spencer. He began some tests, and when Zack told him that he would be able to visit both his parents in the same night, but Spence discovered that he would not be able to control it in the future.

During an election with Gwen, Cam and other candidates, Zack and Spencer did not know who to vote for. Spencer decided to try an experiment with Zack by putting him in a tub of water and see what Zack does during his sleep, and what kinds of interesting material is in his dreams. In his dreams, Zack visits a world where it was only black and white, and everyone was the lame, and the same. No one wanted to exaggerate anything, and Zack had done many things that were against the law, and Zack became a rebel. He refused to eat Mush for breakfast or lunch, he did not want to follow anybody's instructions and dress the way they did, and Gwen, Cam, and Spence tries to figure out how to make Zack one of them. Spencer and a young boy, who was thought to be a rebel (and admired Zack) helps Zack in his campaign in the election after they were convinced of Zack's Other World. Zack finds a red rose, and the smell of the rose made everyone happy, and now they were free, and they wanted to do

Zack's fear of growing up causes him to regress back to childhood when he discovers that he is going to have a Bar Mitzva Celebration at his church. Zack actually transformed back to when 7 years old, and he started acting like a child while Spencer try to figure out how to get the teenage Zack back. Zack's Bar Mitzva was getting nearer while Zack stayed in school and fooled around, causing trouble for Spence and Cam. Spence needed to make Zack feel more grown up and ready to accept the responsibilities of a boy who is becoming a man.

During the robot creation contest, Zack found out he was looking at something else when he put on a special kind of glasses that Spence was going to use for his robot. Spence's challenge was to win the contest with the robot's ability to ""burp"" the alphabet, and a big contender was Gwen, who made her robot play the violin. Zack discovered that someone was sabotaging Spence's robot. Zack had to wear the ridiculous glasses all day to see if the sabotager strikes again. Spence decides to stay beside the closet, which hold his robot to catch whoever is damaging his robot. The trio believed that Zack was seeing through Gwen's eyes with the glasses, and he was seeing Gwen destroying the robot. So is Gwen the dismantler?

Zack falls into Mr. Munk after walking through the door, and Zack just disappeared and he finds himself inside Mr. Munk's body. He was controlling every movement of the headmaster's body. He gathers up his team, Spencer and Cam and tells them the great news. He started his fun by getting Vernon in trouble, and then, he told the students that that they could fool around during breaks between classes. He then returned to Mr. Munk's office, and continues to document fake and funny information about Vernon (such as picking other people's noses). Mr. Mantueffel arrives at the school and inspects the school and announced that the school would be shutting down due to the Headmaster's poor job at keeping the students under control. Zack, Spence, and Cam who did not want to be separated to put in different schools, tried to devise a plan (getting Zack to transform back from Mr. Munk), but nothing could stop the children's havoc. As a last resort, Zack read a discipline book, and used it t

When Zack was practising playing the guitar, he was given a chance to try on Spencer's interactive gloves which gives him a feeling of playing a guitar. Then the gloves began to go crazy, and Spencer was able to release it from Zack's clutches, and they discovered that Zack became an amazing guitar player but he can only play well in his room. When Cam sent Zack's guitar-playing video, it attracts a famous music star who is looking for a member that would replace him in his band. Zack's father gave Zack a new and better guitar while Spencer discovered that Zack was playing so well because of magnetic fields in his room. When this star arrives at Zack's house, he began treating Spencer extremely badly. Zack did not want to become a rock star but Cam kept on pushing him because of money. During the recording sessions, Zack's father came through the door, and disturbed them. Ricky Dallas (the famous star) went ballistic and told ""the old man"" to leave them alone. Daniel Greenburg told e

Zack discovers that his life is a reality TV show, seen on another planet. One of the crewmembers of viewing this show visits Earth to tell Zack that he has bad ratings and Zack has to make sure that he continues to receive viewers or his planet would be wiped out. Zack must try to pick a fight with Vernon, Cam has to go on a date with Gwen, and Spencer needs to make more interesting experiments so they would be more exciting. Each one of them gradually disappeared because there was no use for them anymore. Everyone failed and their civilization would be annihilated but the alien discovered a new and interesting talent from the School Board Inspector.

As the Season Finale, Zack's records were sent out the window when he participated in a fight with Vernon, and Zack lost his entire memory. Zack's friends must retrieve the Zack Files and tell him all of the most important Zack Files to give Zack a chance to retain all his memory. Clips of previous episodes in Season One and Season Two were viewed in attempt to get Zack to become himself again, and once he saw his record files that Vernon had retrieved to announce to Zack that he was one of Vernon's minions, his memory was restored.