At detention, Daniel pretends to be asleep, causing Mr. Right before the group gets ready to find them, Lily warns Emma about the dangers if she breaks the continuum again. Andi speaks with Agamemnon, so she can become a guardian. When Iridium High starts their third year, Lily, who is working to become Jax's guardian as his dad isn't committed to the spot anymore , tells Jax to cast a test spell, and he makes lilies appear for Lily, but she is allergic to lilies. Meanwhile, Diego tries to cheer Maddie up about losing her powers, but Katie convinces him to use his powers anytime Maddie casts a spell so she will think that her powers are back. Diego helps Maddie in everything and Maddie at the same time starts to realize she likes Diego, but they get in a fight after Diego refuses to steal someone's homework for Maddie's benefit. One of the council member, Ramona, disappears and gets trapped, so the council chooses Lily to be the new member.
Daniel says they should wait for Jax, so he goes to find him, and Gigi goes with him. Every magical being starts to get sucked including Emma, Jax, Desdemona, the Hex, Agamemnon, Maddie, Ramona, Lily. Later,Jax discovers his mother is still alive and is bound to find her. Daniel has a talk with Mia at lunch and break-up with her. The Panthers give Andi a portrait of them with Diego, and after everyone else says their heartfelt goodbyes, Andi goes through the portal and teleports to a ruined area.
The battle goes under way and Maddie shows up to watch. After the Cristal de Caballero was put back together, spereating Emma and Maddie, Emma says something to Andi while holding the crystal that makes her invisible. Desdemona and Agamemnon realize they both lost their powers. Meanwhile, Jax's father is revealed to be forcing Jax to use Emma to take over the magic realm. Back at the sanctuary, Diego is looking at a spider habitat when he sees a stone with the Kanay spider marking on it. They meet his mom, Christina, who Emma already knew.
Ursula and Francisco finally share their first kiss. Mia shape shifts into Emma and walk over to Daniel, kisses him, sending a black spider tattoo to the back of his neck. Andi and Jax break into Francisco's office. At the end, Mia gets out, and has Emma, Jax, Andi, Maddie, Diego, Phillip, trapped, as well as Daniel, but she states she's trying to get them out of there. Andi and Mia best each other, leaving Andi tied to the wall in spider webs and Mia stuck to the floor.
He explains he saw another one, meaning, at one point, Kanays were around that area. A little while after they leave, Hex brings Phillip Andi's zombie boyfriend from season 2 back from his video game. At the end of the episode, she says that she needs someone more powerful, like Jake, leaving Jax's face in shock. Lily and Christina are hanging out when the Council shows up and freezes Christina momentarily to tell Lily that her closeness with Emma is clouding her judgment. Later on, Emma gives Daniel his memory back after he says how she is familiar to him.
Christina keeps Lily company while Daniel talks Jax and Emma on one air boat and Andi takes Katie, Sophie, and Gigi on another. They go with Ursula to the airport to watch Phillip leave, and come back to have a group hug. However, when Daniel leaves, the flowers appear around the campus, revealing that Emma still has her powers. Also after the defeat, Emma and Maddie check if they still have powers, as they used them all to send the Principal away. Maddie continues to hide from Ursula that she is dating Diego. Jax and Andi are in trouble when Francisco catches them in his office smashing open the wall in his office, but he leaves early after he is called to go out to the parking lot. Andi goes to Emma's house where she already unfroze Francisco, and they have a meeting with The Panthers and Diego.
Before they set out, Gigi gets stuck in the trap with Sophie and Katie. Meanwhile, Jax is trying to protect Jessie and his mom Liana from Jake after he stopped by just a couple hours earlier. After he sees this, their problems are fixed. At the Beachside 7, Daniel was about to tell Mia about Emma and Maddie's secrets, but Emma walks in and stops Daniel. When Gigi plugs up her equipment for her live stream, she causes a power outage, and everyone sees Sophie with a zombie makeup and run; they then realizes the creature was Sophie when the boys use their trap to capture her. Emma decides to bring back the Principal from season 1 to take her powers away from her.
She soon has an ache in her stomach, so Jax tells her to come back to their house, she does, and it turns out that she was finally getting her powers. Gigi is already fawning over him, but he seems okay with it. Daniel sees this and gets jealous, deciding to do anything to win back Emma; Maddie, Diego and Sophie plan a surprise party for Katie, but she thinks that they want her to make new friends. Van Pelt shows up as well not knowing a thing about what happened, Emma tells them she accidentally froze time. Emma is working for Diego serving smoothies and drinks. Christina comes by before they leave to give Daniel Billy the snake.