Grougaloragran, a mysterious and ancient entity, appears one with a baby carriage. After defeating a mysterious foe with powers over time, who wants Grougaloragran's life force, or "Wakfu", Grougaloragran comes across Alibert, who is quitting his profession as a bounty hunter after almost taking a innocent man to jail. Grougaloragran leaves the baby carriage with Alibert, believing that he will be a good father to the baby inside. He also leaves a message for the adoptive father, along with a baby Tofu (Bird). 12 years later, Alibert has opened an inn and established a small town. The boy, now called Yugo, believes himself to be a ordinary boy until he discovers that he has the ability to create portals. He puts it to the test when a monster rampages though town, ending up at his Inn. Ruel, who was passing though town, teams up with Yugo and defeats the beast, which turns out to have been a Iop possessed by a demon trapped in an item, in this case a sword known as a Shushu. Alibert, seeing Yugo's power, decides to tell him the truth: that he is adopted and that his real family is out there somewhere.

The group comes across a village of Puddles, cephalopod-like gelatinous creatures that turn into puddles. They are constantly attacked by a pack of Taures Bullies, wild bovine beasts that constantly raid their village for food. The group manages to fight them off, but know they will return as they always have. Not wanting to turn a blind eye to turmoil, and needing food themselves, the group decide to help train the Puddles so they can be ready for the next raid. The Bullies attack again, but the group, along with the Puddles, quickly overpower them. However, the Bullies brought one of their leaders, their father, Mandhal the Mighty. He proves to be a tough foe, even having his own beam attack, but Yugo uses his portal to deflect Father's beam attack back at him. With Father defeated, and worried about Mother finding out, the Bullies flee, leaving the Puddles to live in peace.

Lost, the group finds themselves in front of a tower belonging to four sisters who wish to find the perfect husband. Percedal, completely smitten just by the top of one of their heads, climbs up to get a kiss. When he gets to the top, he finds that the sisters are actually ugly because of a curse put on them after the picky girls had ridiculed every single suitor. To be cured, one of them must be kissed by a man, and they hold Percedal captive until they get their kiss. The group dons disguises to get inside the tower. The nine of them decide to hold a little contest to see who will get the kiss from Pinpin, which ends up being pure torture. Things quickly go wrong when Eva enrages the sisters and causes them to attack the group. Freeing Pinpin, the group flees with the aid of one of the sisters, who believes that they got what they deserved and is sorry for what they did to Pinpin. As they flee, Pinpin blows the sister a kiss, which turns the sisters and their tower back to normal.

Following a very delicious smell, the group finds a man attacking a beast made entirely out of bread. They mistake the man for the attacker, only to later find out that the man, a innocent baker named Xav, was attacked by Breadnaughts who were after the rare Golden Wheat stored in his barn. Before the attack, Xav was going to enter a bread baking contest with the special wheat which is thought to produce exquisite bread. Wanting to fix their mistake, Yugo decides to help Xav make the bread while the others harvest the wheat. They enter the competition and with Yugo's help, Xav wins. The Breadnaught inadvertently reveals that she is Chouquette, Xav's father's former apprentice, and that she was after the wheat because she is in love with her master and wanted him to win.

Yugo and his friends fight through a dungeon to find a boat but they don't get what they expected.

The gang continue their journey to the top of the tower. At the Feca floor, they encounter a demigod named Bump. He is willing to let them pass without fight, but he has a peculiar condition: he wants Yugo, Ruel and Amalia's pants to add to his underwear collection.

The gang and Kriss Krass play Boufbowl to save him from losing his head.

Ruel bets with the owner of an inn that he and his companions can stop the Voice Thief.

The gang, traumatized by the time bubble, enter Oropo's tower to rescue Eva and Flopin. Inside they meet an Osamodas girl, who tries to convince Elely that Oropo and his brotherhood are actually good.

The village is attacked by Polters, creatures that turn humans into shrubs, Yugo and his team go to the Forbidden Forest to find out why the Polters are doing this. Inside they encounter the ruler of the forest, the Soft Oak, who plans to turn all humans into trees in revenge for the destruction his forest has suffered. Amalia, a member of Yugo's party, convinces Soft Oak that not all men are like this and that only free men can protect the forests. She then heals him with magic and he agrees to turn the shrubs back into humans. In the village, Yugo and his father are attacked by the time villain from 12 years ago, now revealed to be a Xelor named Nox. Nox manipulates time to age Alibert rapidly and he calls Yugo a Eliatrope, swearing to get Yugo's Wakfu one day. Alibert, knowing that Yugo deserves to know the truth, tells him that his real family, the Eliatrope race, are out there somewhere at a place called Oma Island. Yugo's friends agree to help him find his real family and stop Nox and set off for the adventure.

The group goes to Kelba's market in search of a map to begin their quest. When they arrive they find the marketplace under attack by the Black Crow. The groups learns about a shop run by Kabrok, a old adventurer who hung up his cape and became a stock boy, and Miranda, who is Kabrok's strict, but loving, wife. They have a map the group can buy, but are unable to sell thanks to the Black Crow. The heroes lay a trap for the Black Crow and are able to take him down. The Black Crow is revealed to be Kabrok, who was bored with his life, craved adventure again, and felt that attacking the local merchants was the way to get it. Kabrok and his wife sell the group a map.

Amalia is bitten by a poisonous Red Rose. Ruel says that his old friend, an Eniripsa named Nausica, lives nearby and can help heal her. They learn that the only cure to a Red Rose bite is sap from the rare Severum tree, which is located deep in the nearby Maleficent forest. Ruel and Yugo leave to gather the sap while Percedal and Eva stay behind to help care for Amalia. Not long after Ruel and Yugo leave, Amalia's doll goes berserk, attacking Nausea, Percedal, and Eva. It merges with Rubilax, turning into a monstrous demon. The trio overpower it, forcing Rubilax out and cutting the doll up into pieces, but the pieces turn into other dolls and attack in masses. In the forest, Ruel and Yugo are attacked by giant Venus flytraps, but are saved by a forest dweller named Sybannak. They are forced to help her in exchange for the sap, but when the tasks become tedious and monotonous, Ruel instead decides to steal some sap. Enraged, Sybannak attacks with the Venus flytrap monsters. Rue and Yugo escape with the sap and return to Nausea's where they save Amalia and return the dolls back to normal.

Yugo, Amalia, Ruel, and Elely arrive at the Ecaflip floor of the tower. Its protector is Kerubim and Atcham's brother, Ush. Being an Ecaflip, he loves to gamble and invites the gang to play a deadly game.

Arriving at the Enutrof floor, the gang find four doors, so they decide to split up in order to find the exit quicker. Along his way, Ruel reminisces about his youth and a girl he once loved named Arpagone. Ruel encounters Arpagone, who takes him captive so that a fake one can infiltrate the group. The Fake Ruel converses with Yugo about his love for Amalia, wondering if she'd ever feel the same ever she ever stopped the stubborn princess routine.

Yugo, Amalia, Elely, and fake Ruel arrive at the Sadida floor wherethey meet the Demi-God of the race, revealing that she doesn't want to fight, but to talk. She discovers the Fake Ruel among their party and captures him. Arpagone tries to convince the real Ruel to join her and Oropo. Evangelyne and Flopin manage to escape their prison but are intercepted by Toxine and Echo. Echo tries to persuade them to come back, but Toxine electrocutes her and chains her up as her hate for Echo trumps everything else. She goes into a sadistic fight against Flopin and Eva and they somehow manage to fight her off but launching her into a Well of Shadows – a representation of her own soul, dark, evil, and chaotic – but she fires an energy bolt as she falls in, striking Eva in the womb and electrocuting her.

With no other route to take, the group is forced to pass though an inhospitable town full of decay and zombie-like townsfolk. Vampyro, a vampire, comes to claim Eva as his wife, by using a magical ring to take her shadow, i.e. her soul. The group launches a rescue mission, avoiding ghouls launched by Vampyro. While scaling his castle, the group is overrun by vampire bats. Percedal volunteers to stay behind while the others go to rescue Eva. They arrive and find that Vampyro is using Eva's body as a vessel for his true love, Shadofang. Vampyro uses his shadow stealing powers on Ruel, turning him into a beast that Amalia eventually defeats. Amalia, Yugo, and Percedal fight Vampyro, but he proves to be too powerful. However, during the fight, they discover his weakness: he's allergic to Az, their mascot. the group uses Az to their advantage, overpowering Vampyro and getting the ring off of him. He turns back to his original self, a magistrate named Wagner. His release also turns the town and the townspeople back to normal and returns the shadows of Eva and Ruel.

Yugo is reunited with his father. Evangelyne believes that Percedal isn't dead and that she hears his voice. Ruel gets in trouble while looking for treasure underground.

The group starts their new adventure by taking a cable car and has to defend it against some black ravens.

Cléophée, Ruel, Sadlygrove and Yugo search for a boot but get into trouble with some pirates.

Ruel plays dead to find a legendary treasure and the gang saves another pair of lovers.

Ruel & his team, Real Gobbly, along with Percedal, play against opposing team, Lamechester United, led by professional gobbowl player, Kriss Krass.

In the course of their trip at sea, the five friends encounter a terrible tempest and their boat is wrecked on an island. Yugo, Amalia and Evangelyne disembark in search of food, but primitive Sadida take them in hostage: these are Kaniboules! And it seems that they have the poor habit to give the foreigners in sacrifice in their godhead: big Moon... This smells bad for our heroes!

On their way back to Sadida the gang angers the legendary Dragon-Pig.

Yugo and Adamaï try to learn more about their people by activating the Eliacube but accidentally free Qilby.

Knight Justice takes Yugo and his friends prisoners because he holds them responsible for setting Rubilax free.