Alex takes on an internship with a top Fashion Magazine and decides to put on an outrageous fashion show featuring Harper's bizarre wear to teach her boss a lesson for taking credit for her ideas. Jerry and Theresa hire a new girl, Millie, at the Sub Station that Justin immediately falls in love with so Max tries to help.
The kids fail at their group magic project, so Jerry devises a plan that will force them to work together. Now Alex must wrestle with sacrificing her first one-on-one date with Dean so that she and Justin can help Max's superhero, "Maximan," solve the crime and prove to Jerry that the siblings can work as a team.
Alex tries to avoid running into Harper at the annual Comic-Con type convention in order to protect her wizard secret but winds up revealing the truth after Harper takes a spin in Alex’s power laden Battle Diva costume. Meanwhile, Justin and Max work alongside Hugh Normous and the Emergency Wizards to make sure other wizards don’t perform any real magic.
When Mr. Stuffleby, a wizard guidance counselor, informs the kids that they must have a viable profession to fall back on in the event that they don't become wizards, Max chooses to become a street magician while Alex and Justin decide to form a band. They all test their skills by hosting a Waverly After Dark performance at the Sub Station.
Alex gets the lead as Tinkerbell in the school's production of Peter Pan but doesn't want the part. So when she enlists the help of a real fairy to sub in and play the part, it causes the production to get out of control and the play is not necessarily performed in the same way as the traditional Peter Pan fairytale!
When the Russo kids discover that their lives are being exposed in the form of novels written by popular author H.J. Darling, they travel through the Inter-Wizard People Porter to confront her and learn that Ms. Darling is Harper from the future. Justin must then work to ensure that Alex remains friends with Harper to preserve the outcome of their futures.
When Alex, Harper and Justin are accidentally transported into a silent movie, Justin and Harper begin to recognize a closer bond between them. Things heat up at the restaurant when Theresa and Jerry begin arguing about who has the more difficult job. To determine who's right, the two switch places.
The episode "Cast-Away (To Another Show)" is the first part of a three-way crossover that continues on The Suite Life on Deck and concludes on Hannah Montana. Justin takes Alex and Max on a cruise to Hawaii aboard the SS Tipton when he wins tickets. He pretends to be a doctor to impress London Tipton while Alex uses magic to bring Harper on the ship. During the cruise, Alex pulls a prank on Justin that turns him blue while Hannah Montana boards the ship to attend a concert in Hawaii, leading Cody to try and get tickets for himself and Bailey.
After Dean moves away, Alex continues to date him by using magic to enter his dreams. When he pays her a surprise visit and the real date isn't as great as she had dreamt, she searches for a way to break up with him. Meanwhile Justin tells his vampire girlfriend Juliet that he is not allowed to go on her family camping trip.
Jerry and his siblings, Kelbo and Megan (Jerry revealed to the kids they have an aunt), need to retake the Wizard test that, in their teen years, determined who got to keep their powers. When Alex, Justin and Max see how competitive the contest gets, they realize the same test could eventually tear their family apart as well.
The Russos go on vacation to the place where Jerry and Theresa met. An unhappy Alex wishes her parents never met, activating a spell that makes the wish come true. This puts the entire Russo family's existence in jeopardy. To reverse the spell, Alex and Justin begin their search for the Stone of Dreams. While Max is trying to get Jerry and Theresa back together.
Justin is summoned to track down a scary mummy as part of his monster hunting duties. He and Juliet set off to the museum to track the monster, but things take a turn for the worse when Justin and Juliet become trapped in the museum. Meanwhile, Alex tries to separate Max from his conscience after he starts excelling in his wizard studies.
When Harper learns that her family is moving away, the Russos offer to let Harper live with them. While Alex and Harper clean out the basement to make room for Harper's stuff, Alex shrinks herself down to fit in her old doll house, but Jerry and Theresa give the doll house away to a little girl named Olive with Alex still in it.
Justin’s chances at becoming Student Body President are put in jeopardy after someone wallpapers Principal Laritate’s office with posters from Justin’s campaign and he is accused of masterminding the prank. Meanwhile, Alex befriends Stevie, a rebellious new girl in school, and Jerry, Max and Harper get stuck on a Ferris wheel during their trip to Coney Island.
Harper is desperately trying to remember something, but she cannot. Alex offers to help Harper recall her memory, so she casts a spell on her. Harper then remembers: Stevie is a wizard, and she saw her cast a spell. Alex and Harper confront Stevie, and she confirms their suspisions by casting a spell in the ground that opens up a warp hole and a student falls in. Alex is happy that she has a wizard friend, but Harper feels left out.
When the school's superintendant fires Mr. Laritate because of Alex, Mr. Laritate gets a job at a western place. When the school hires a strict new principal, Alex transports Mr. Laritate back to the Old West in an attempt to show him that it's not what he thought it was and make him want to come back to Tribeca Prep.
Harper and Alex find out that Max has a girlfriend named Nancy Lueke, but has been keeping it a secret so not to get embarrassed by his family. Later his mother finds out about it and tells him that it's not okay to hide the truth from anyone. Since he took his mothers advice, he tells Nancy his secret about being a wizard. The Russos make up another lie to cover the truth, and Nancy breaks up with him.
Alex is punished for buying a vending machine with her parents money. Alex sees a mirror that says "Do Not Go In Alex". After Alex steps through a magical mirror, the universe becomes all about her, and when the mirror breaks after she doesn't want to come back to the real world, Alex is possibly stuck in the parallel 'you-niverse' forever.
Wilmer Valderrama guest stars on Wizards of Waverly Place in the episode 'Uncle Ernesto'. Uncle Ernesto has no idea that the Russo's have magic abilities, so they promise a magic free night so that he can come over for a birthday dinner. Meanwhile, the kids get a magical chicken that can tell them the answer to anything. They ask it the age-old question, "Which one of us is going to win the wizard competition?" But when the chicken runs amuck, they have to catch it before he lays the answer and Uncle Ernesto finds out about magic.
While watching a news broadcast, Alex discovers that Mason (in wolf form) is in the Poconos Mountains trapped by country wizards. The country wizards will only give back Mason if Alex trades them their portal. Alex then discovers that the country wizards have turned Mason into a half wolf form. But can she live to be with Mason like this without being embarrassed by him?
Alex joins Justin's wizard class to try to move up in the competition. Max joins a sophisticated wizard society. They suggest he move the wizard competition up and he moves it to a few days away. Max quits the society because he finds out that they are taking advantage of him. Alex and Justin transform into Max in an attempt to change the date of the family wizard competition back to it's original date and succeed. In the end of the episode they accidentally turn Max indefinitely into a little girl.
With Max still a little girl, their parents pay more attention to Max (Maxine), and Alex becomes jealous. Justin takes Maxine to her (Max's) karate class and Maxine kicks Justin's butt. After the class, Alex decides to make Jerry's favorite sandwich in order to win his love back, but Maxine comes along with Justin, announcing that she beat Justin in karate, and Jerry immediately falls for her cuteness again. More jealous than ever, Alex comes back with Justin to Maxine's karate class with their parents, having a slight idea of knowing how to change Maxine back to Max. They cast spells on Maxine, Justin using the spell he used on Max that turned him into Maxine, and Alex using the reverse spell. Unfortunately, it only makes Maxine cuter, which makes her furious. Instead of going against the person she was supposed to, she demands that she kicks either Alex or Justin's butt. Justin goes against her, but seeing that he would lose, Alex casts a spell on Justin to make him a karate master. Too fast for Maxine, Justin beats her, and Maxine is hurt (physically). Jerry and Theresa rush to her side, caring for Maxine more than they care that Justin beat Maxine in karate. Justin leaves, and Alex leaves after him, heartbroken. Back at home, Jerry tells Alex that he fell for Maxine because she reminded him of Alex when she was little and they bond again. Meanwhile, Zeke thinks the Russos hate him, but really it was just Harper's alibi in order to keep him away from the Sub Station so as not to make him suspicious about Max's disappearance and Maxine's appearance.
Justins and his delinquent class have a wizard wand dance assessment to do which will get them back in Wiztech, though a new student named Rosie joins, Justin falls madly in love with her to later find out she's an Angel. Meanwhile, Jerry, Teresa and Harper try to think of ideas of how to get more people to come to there restaurant. Harper makes cards which get hole punched each time you buy a sandwich - when you get 9, you get a free sandwich. A man though punches his card at home and demands a free sandwich. They use Maxine's charms to make them go. After Alex gets Rosie to rejoin Justins class since Justin had to kick her out other wise they would have failed, Alex gets Rosie to come back and puts a copycat spell on her, though it goes wrong when Alex panics when a bad animals on her foot and Rosie copies. The Wizards fail but Rosie and Justin start dating.
Rosie is an Angel of Darkness (fallen angel) and has been deceiving Justin all along, to Gorog's plan. Alex finds this out with the help of Tina (a guardian angel in training) when she goes to the Angel Realm. Justin crosses over to the dark side with Rosie and becomes an Angel of Darkness, breaking his wand. He steals a special compass from the Angel Realm known as the Moral Compass, and now the leader of dark angels, Gorog, wants to destroy Justin since he's an outsider. Rosie, realizing she was deceived by Gorog as well, comes to her senses and tries to get Justin to run away to save him, but Justin refuses. With angel wings, Alex tries to convince Justin that he should not be an Angel of Darkness, because in his heart he was a good wizard. Meanwhile, Maxine is forced by Harper to have a slumber party, since Harper never had a slumber party. Maxine gets mad and turns all of the girls into "older guys".
Professor Crumbs is planning to check on the Russo's to see how their wizard training is progressing. This causes Alex and Justin to panic since they don't know how to explain "Maxine", and they try to find a way to turn Maxine back to Max. Meanwhile, "America's Got Talent" runner-up Jackie Evancho sings at Tribeca Prep's "Spirit of America Play", which gives Harper a run for her money as she takes the stage for the first time.
Alex has been crowned Wizard of the Year after saving the world from dark angels, as well as being reinstated in the Wizard Competition, and a banquet honoring her achievement is hosted. With paparazzi in tow, Chase Riprock visits the lair to congratulate Alex. As he leaves, Keith Keith hounds them about being in a romantic relationship, to which Alex states she already has a boyfriend. Later, Mason and Alex watch his gossip segment, and to their horror, Keith Keith confirms that Chase and Alex are dating. For Alex winning Wizard of the Year, the Russo family must record a holographic video congratulating Alex, however, much to Justin's displeasure, Justin's video instead only contains him complaining about Alex. The night of the awards banquet, Mason stands Alex up, leaving her devastated. At the banquet, Chancellor TootieTootie tells Justin that his display of affection and pride for Alex may reinstate him into the competition, causing Justin to be frantic and do everything within his power to destroy the tape. Chase purposely invites himself to sit at the Russo's table. However, Mason shows up late and sees Alex and Chase flirting together. A short battle ensues between Mason and Chase. Alex soon breaks up the fight, and is forced to choose either Mason or Chase. Appalled by both of their behaviors that evening, Alex chooses neither and breaks up with Mason.
The Russos head to the beach on an extremely hot day, and Harper hopes to enjoy reading her book while at the beach. The Russos come across Zelzar, a fortune-telling machine. Jerry warns the kids about Zelzar - he is from the wizard world, and a wizard's fortune really comes true. After Max and Justin receive good fortunes, Alex decides to get a fortune despite her father's warning. However, her fortune says, "Say good-bye to your life." Alex thinks nothing of it and proceeds to enjoy the day at the beach, but comes close to life-threatening situations multiple times. Alex, Justin, Max, and Harper make a compromise with Zelzar - if they can extract him from the machine and let him enjoy a day at the beach, he will take back Alex's fortune. Max replaces Zelzar, and Justin is forced to drive the beach-goers away from the machine (as Max gives out silly fortunes about his new facial hair); meanwhile, the girls help Zelzar fancy his day at the beach. In the end, Zelzar reveals that while he cannot take away Alex's fortune, he can give it to the next person. The next person happens to be a little girl, who gets Alex's fortune. However, it is revealed that a man from Random Prize Giveaway shows up, saying: "Say good-bye to your life because we're randomly giving you one million dollars!"
It's finally time for Justin's delinquent class to take their finals, which will get them back in to Wiz Tech and Justin back into the Wizard Competition. But when they fail, Justin blames Alex; Alex knows they knew their stuff and that she didn't cause them to fail. She investigates and finds the real reason, as well as the owner of the most powerful wand in Wizard history. Meanwhile, Teresa and Jerry find that they saved nothing of Max's childhood and seek help from Harper to recreate it.
Alex and Harper decide to move out and live on their own but, they need the money to buy one first. So, they they decide put on puppet show to get money. But, When Alex doesn't keep up her end of the bargain she and Harper have a fight. Meanwhile, Max might loose his girlfriend when Thalia's parents don't like his parents.
Alex and Harper decide to get another Roommate after they learn having an Apartment takes a lot of money. So, they find Lucy, a Ghost who is heart broken after her boyfriend disappeared over the Bermuda Triangle. So, Alex and Harper try to set her up with Justin but she ends up going on a date with Mason. Meanwhile, Even though it was supposedly lost Justin and Zeke's Robot has arrived and Zeke thinks it is evil but, Justin won't believe him. Note: This is part 2 of a 4-part arc.
After Dexter reveals himself as Gorog, the angel of darkness, he turns Felix evil in order to use his powerful wand to take over the Wizard World. Alex, Justin and Max learn from Professor Crumbs that they must use their wizard powers together to defeat Gorog and the dark side. Note: This is part 4 of a 4-part arc.
The Russo family and friends are headed to Tuscany, Italy, to meet their long lost relatives... but when Alex tries to prove she's more than a seemingly carefree young Wizard, she inadvertently conjures a spell that creates a Good Alex and an Evil Alex. When Evil Alex gets roped into a charming young wizard's foreboding plan to take over the world, Good Alex must find a way to save her family and humankind, which leads to a monumental battle between the two versions of herself - all atop the Tower of Pisa.