On her way home from school Alex Mack is practically hit by a truck. The truck is carrying a top-secret chemical and spills it on Alex. Alex learns later that she has magical powers and shares this secret with her sister, Annie, and best friend, Raymond.

Alex and Raymond are continually harassed by upperclassmen Jessica and Ellen. One afternoon Jessica trips Alex in the school cafeteria as Alex carries a tray full of food. A food fight ensues and Vice Principal Heller assigns Alex, Raymond, Jessica and Ellen to clean up the cafeteria every afternoon. Both sets of friends blame each other for the trouble, and they agree to take up Raymond's challenge of two-on-two on the basketball court. The stakes: the losers have to admit responsibility to Heller and clean up the cafeteria by themselves.

The big dance is just around the corner and Alex still hasn't been asked by the only person she cares to go with. Everybody knows she dreams of going with Scott, but he's not the one hounding her for a date. Jerry, an obnoxious, insensitive and persistent ninth-grader is relentless in his pursuit of her. He won't take no for an answer, but Alex continues to put him off.

Annie's science project has been chosen as a finalist for the big science fair to be held at the Paradise Valley Chemical Plant. The whole Mack family is looking forward to spending Saturday at the science fair rooting Annie on, except Alex. Not only is she sick of witnessing Annie's triumphs, but the chemical plant is the worst place for her to be. It's crawling with plant spies who are constantly on the look out for "the kid."

Alex and Ray have a falling-out and Alex is afraid Ray will disclose her secret to the plant.

Alex and Dad have trouble connecting. They go on a day trip together and chaos ensues.

The plant closes in when Alex's journal, detailing her powers, ends up in the wrong hands.

Alex steals a test to help Nicole, who is cracking under the pressure of the exam. At the plant, George discovers that GC-161 has the capability to alter human genetic structure.

After a collision with a pole during a baseball game, Ray gets superpowers and goes public. He even negotiates an endorsement deal with the plant. When Ray finds himself trapped and submitted to test after test, he uses his powers to escape from the plant.

Alex and George discover that gifts and decorations aren't as important as the Christmas spirit, while Dave's gift to Vince is a chimp that runs amok in the plant.

Alex is split into two manifestations of herself when George discovers a chemical that divides GC-161 into its individual elements.

The evil Alex wreaks havoc with her friends and family while Annie and Ray try to find the good Alex to recombine the two.

Alex becomes a photographer on the yearbook staff to earn extra credit. Louis develops a crush on Annie when she tutors him. Alex uses her powers to get herself paired with Scott on a photo assignment.

Alex experiences a chemical reaction to GC-161--uncontrollable bubbles. This unusual development coincides with the demise of Annie's relationship with Bryce.

When Alex and Annie are stuck at home during a rainstorm, they reminisce about the value of superpowers and sisterhood.

Alex saves a woman's life but can't tell the authorities that she double-morphed the woman to the hospital. The mystery heightens Danielle Atron's suspicions. As Annie prepares for college, a bittersweet realization comes over the sisters who share so much.

After four years of keeping her powers hidden, Alex's secret world is falling apart. As the Plant prepares for the release of GC-161 to the public, her dad loses his job, and Louis discovers her secret powers, and is captured by the Plant.

The final episode. Ray, Louis, and Hunter try to free Alex and her parents from the Plant which is lined with bombs thanks to Danielle Atron. Meanwhile Dave works with Gino and the FDA to stop the chemical plant from releasing GC-161.