The Shadow Phoenix is the fourth and last one-hour special from Nickelodeon. It was based on Second Season. This special reunites the episodes 1, 2, 3, 5, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25 and 26.
The special starts with the Winx and the Specialists sharing a moment of peace, and commenting about how good is that everything is back to normal, without the Trix causing troubles. Meanwhile in a cave, there is a fairy named Aisha who is climbing rocks, saying to herself that she has to save the Pixies. The fairy finally reach the place where the Pixies are captive and she release them.
Unfortunally, Aisha is stopped by the Shadow Phoenix (Lord Darkar), who steal the Pixies away from her again and defeat her by pushing her to a cliff. Back to Alfea, the Winx are saying goodbyes to their friends from Red Fountain, then Flora sense something coming from the trees and Bloom goes to see what is, the Aisha appears exhausted and faints.
Later, Aisha awakes and tells the Winx about the Shadow Phoenix and the Pixies that must be recued, the five students of Alfea are agree to help her new fairy friend. Bloom and Stella are chosen to asist Aisha in the mission, because they powers are more effective against darkness. The Specialists carry the three fairies to the Under Realm closest as the ship permits. Aisha, Bloom and Stella continue the rest by themselves. Everything appears to go well, until the Trix appears with new powers and defeats the three fairies, but the witches are stopped by a mysterious winged man. Aisha reunites with the Pixies and two of them, Lockette and Amore respectively bonds with Bloom and Stella.
Back to Alfea, Tune along with Chatta and Digit also form bonds with Musa, Flora and Tecna. In the morning, Faragonda told Aisha that she spoke with her parents, so the fairy can join at Alfea, the headmistress also introduce a new teacher, Professor Avalon. Stella, Bloom and Aisha instantly recognice him as the winged man who help them during their mission on the Under Realm.
During the night, Bloom awakes after having a dream about her family. In the morning, Stella coplains about the rain, until a flower appears in front of her and the other girls. Professon Avalor appears saying that is a gift and ask Bloom to come see him latter, because the dream she has. In Avalon's office he ask Bloom to empty her mind, then she gets a glimpse of her biological parents and the great dragon but before Bloom can reach them, a dark fog blocks her way and attacks the fairy causing to open her eyes.
Later, the Winx goes to Red Fountain, there Flora meets Helia. Meanwhile Sky is concerned about Bloom who looks like she is under spell. The following day, Sky calls Bloom on her cellpone but the fairy only comments about the good qualities of Professor Avalon and Sky says is tired of her crush with the Professor, that upsets Bloom and tells him to cut the phone, he does it. During one of Palladium classes, Flora is having a daydream about her being saved by Helia and marrying him. Outside Alfea, Bloom is training, Avalon aproaches her and asks if she is ok, Bloom tells him about her problem with Sky.
In other place, the Pixies are playing until someone puts on spell that makes them return to Pixie Village. Then Icy along with some monsters follow the group till the village where Icy freeze and scare more pixies. Without having other choice Ninfea gives Icy the Codex. Later, Avalon took the oportunitty and kidnap Bloom. The Winx report the situation to Faragonda and send the fairies along with the Specialist to save Bloom.
After dealing with Trix, the Winx and the specialists come to Realix but Shadow Phoenix stops them with a spell. Sky manages to stand up, approaches Dark Bloom and tells her to fight for who she really is. Apparently, it did not appear to be useful but Bloom remembered some good times with Sky, which gave her the strength to break the spell. With the Winx together, they made a convergence that managed to defeat the Shadow Phoenix for good. Then everybody leaves the Under Realm and return to Alfea, where a party is held for the victory during the night.