The entire Russo family, except Alex (Selena Gomez), who is to be staying with her best friend Harper Finkle (Jennifer Stone), are preparing for a vacation to the Caribbean. Alex decides to sneak a peek at Justin (David Henrie)'s personal belongings when his enchanted backpack attacks Alex trapping her as Justin had planned. When her father, Jerry (David DeLuise) comes down to help he accidentally speaks of the forbidden book of spells and how he let Justin borrow it, which Alex takes when no one is looking. Alex wants to go to a party with Harper but her mother, Theresa (Maria Canals Barrera) tells her she can not go to the party because she is untrustworthy even with Harper around.
After her parents go out, and her brothers are not in sight, Alex puts a spell on the sub-station train so it will take them to the party (without actually leaving the building since her parents told her she wasn't allowed to), but Alex and Harper miss the party after almost getting killed by a real subway train and running into a dead end tunnel, only to be saved by Justin, using the full-wizard wand to do so. Unfortunately, the side frame of the subway car falls off, just as their parents come back. Because of this, Alex is forced to go on vacation with the rest of the family to the Caribbean, the kids having their wands confiscated. Along the way they meet a street magician and former wizard (Steve Valentine) (who lost the full-wizard contest to his older brother) named Archie who wants to turn his girlfriend, Giselle, from a parrot back into a human by finding the Stone of Dreams, which has the power to grant any wish or reverse any spell. Jerry considers it crazy since many wizards have gone on the quest and never returned.
Later, after Alex was about to use a spell on her mother to convince her to let Alex hang out with a boy, she gets caught, grounded and forbidden to use magic. After a heated argument with Theresa, Alex, in a fit of rage, wishes that her parents had never met; unfortunately, the smuggled full-wizard wand and spell book, which Alex was holding at the time, grants her wish. As a result, Jerry and Theresa do not remember Justin, Alex and Max (Jake T. Austin) or each other.
Alex, Max and Justin attempt to get a spellbook from Jerry by levitating it out of his pocket, but he catches it. Jerry is shown to still have his powers, since he never gave them up to marry Theresa. Jerry has a more carefree attitude with magic due to this change. Justin asks him "hypothetically" what would happen if a wizard wished that her parents never met. Jerry explains how they would gradually forget their past, and then disappear forever. He says it would take a miracle to fix it, whereupon Justin mentions the Stone of Dreams (La Piedra de los Sueños), which Jerry says would work too.
After consulting Jerry, Justin and Alex set off to find the Stone of Dreams, guided by Archie. Meanwhile, Max stays at the resort to keep his parents from meeting other people. Over the course of the day, Max visibly begins losing his memory.
Realizing the possibility of not existing if they don't find the stone, Alex and Justin apologize to one another for all the trouble they caused one another. Along the way, Justin and Alex face many obstacles such as getting across a wide canyon, escaping death from quicksand, and getting across a narrow ledge. Realizing that something is wrong, Max asks Jerry to help him find Alex and Justin, and Jerry agrees after some persuasion. They are joined by Theresa, who believes them to simply be treasure hunting, but nonetheless proves useful, as she is the only one of them who can speak Spanish.
Eventually, Alex and Justin succeed in finding the Stone of Dreams, but Giselle steals the stone. The kids tell Theresa and Jerry their story. Theresa doesn't believe them because she thinks she would never forget her own children. While trying to figure out how to reverse the spell without the stone of dreams, Jerry mentions that if one of the kids was a full wizard, they might be able to cast a spell to reverse it. While preparing to begin the full-wizard contest, Max finally loses all memory of who he is and gets sucked into the vortex of non-existence. Theresa remembers him slightly, and realizes that they were telling the truth. Realizing they must work quickly, Alex and Justin are transported to an ancient battlefield, where the contest will be held. Jerry explains that they will only be allowed to use spells involving the four elements (earth, water, fire, and air). The winner will become a full wizard, and the loser gets nothing while losing their powers forever. Alex and Justin engage in what turns out to be an intense battle, and Alex narrowly wins.
In trying to come up with a spell to fix everything, she turns to Justin for help. However, Justin has lost all his memory (despite the fact that he is older than Alex). In a rare moment of love and compassion, Alex tearfully tells him who she is and that she's his little sister. Alex tells him that even though they pick on each other, she looks up to him and is jealous of him and begs Justin not leave her here alone. Justin tells her that he'd never leave her and that even though he doesn't know her, he believes her, and wants to help, but he cannot and is sucked into the same vortex that Max was. Desperate, Alex tries to cast a reversal spell, but Jerry tells her it may be too late.
Meanwhile Theresa is back at the resort, and seeing that Giselle has returned to human form, with the Stone of Dreams hanging by her neck, tries to get it from her. Archie manages to get the stone from Giselle, who wished to leave him now that she was in human form. He turns her back into a parrot and gives the stone to Theresa. Theresa then wishes to be where Alex, Justin and Jerry are, at which point she is transported to the same battlefield where the others are so she could give Alex the stone. Jerry tells Alex she can wish for her brothers to reappear and still keep her full wizard powers. However, Alex learned that family is everything you can have, and that it's all you wished to have, so she wishes that everything go back to the way it was before, and time rewinds back to the beginning of the argument between Alex and Theresa that started all the trouble, which is quickly stopped when Alex apologizes and accepts her punishments with grace; while Theresa and Jerry remember nothing about the ordeal, Alex, Justin, and Max do. Everyone regardless becomes closer from the events that had occurred, as the kids remember what they went through, and as their parents notice a change in attitude. They happily walk off together as the end credits roll. The credits show the cast dancing and also Jerry wearing a skirt and dress.
