In the Upworld, Jay's coma worsens and he's taken to intensive care, causing Val to be faced with the prospect that her son may never recover. Meanwhile in the Downworld, Jay believes that his connection to home lies in the Tower, so he sets out with his companions to find it.

When 11-year-old Jay Ziegler falls from a treefort after being pursued by bullies who wanted his father's precious telescope, he ends up in a coma - in the real world (known as the Upworld). In the Upworld, Jay's mother Val, his best friend Donna and the bully Keith all try to cope with their reality. In the Downworld (Jay's mind), Jay finds himself in a world entirely populated by children, where he meets up Alpha and Flash (the Downworld counterparts of Donna and Keith) and the trio embark on a mysterious mission involving a telescope, the land's mysterious leader Brad, and a connection to Jay's father.

In the Downworld, when a mysterious girl named Medea, prophecizes that Jay will be the destroyer of their world, she attempts to get rid of him for good. Meanwhile in the Upworld, Keith volunteers to look after Jay's dog, Bentley, when Val becomes too busy.

In the Upworld, when Val is laid off work due to her spending so much time with comatose Jay, she decides to visit her mother in the country at the family farm. At Driftwood, Donna and Keith continue to help by reading King Arthur stories to Jay. Meanwhile in the Downworld, the trio reach a cornfield where Flash meets Lobelia & Yudo and learn of Yudo's belief of ""Big People"".

In the Upworld, Donna and Keith prepare a birthday party for Jay's deceased father, in order to get a reaction from Jay. In the Downworld, Jay and Medea travel into the Lighthouse to rescue Flash.

In the Downworld, Jay finally meets Brad but is shocked to discover he's a 15 year old boy - not his grown father.

In the Downworld, while in search of the third Checkpoint Jay & his friends visit the Brad Exchange, where Brad's supposed belongings are traded. In the Upworld, Max experiments with some of Jay's possessions to see if he responds, and oddly, he responds only to items that used to belong to his father.

In the Downworld, a downhearted Jay spends time in the ""bus-cafe"" but is soon reunited with Flash and Alpha, as they find themselves on the run again, and find themselves near the lighthouse.

In the Downworld, en route to the Lighthouse, Jay and friends are captured by pirates and Flash disappears. In the Upworld Val is forced to go to a lawyer to have Brad declared legally dead, in order to pay for Jay's treatment.

In the Downworld, once inside the tower the trio find that Brad is no longer in power, but instead Macro is running the whole show. In the Upworld, Donna sees images in a mirror that resemble Alpha, Flash and Jay in the other world.

In the Upworld, Max attempts a new technique that immerses Jay into water to isolate his senses. Meanwhile in the Downworld, as he continues to search for Jay, Finger leads his troops to an underground cavern where kid-scientist Fractal is experimenting on a crystal with unknown powers, that causes those who touch it to turn into a zombie.

In the Downworld, Jay and Flash break the telescope, which causes the entire Downworld to be in complete darkness. Meanwhile in the Upworld, when visiting Jay, Keith accidentally breaks the telescope and is forced to repair it before anyone finds out.

In the Upworld, Jay, Keith and Donna become caught up in a group of teenagers who are harassing a shopkeeper. Meanwhile, in the Downworld: Jay, carrying a strange globe, is proclaimed the ""Pathfinder"", by a group of kids in search of their homeland.

In the Upworld, Jay meets with his father, and tries to persuade him to come home. Meanwhile, in the Downworld, as the election campaign begins, Finger develops a plague which freezes the kids into being unable to vote.

In the Upworld, Jay meets Nikki, with whom he shares his experiences in the coma, but is shocked to discover they see the same therapist. Meanwhile, in the Downworld, Finger hires an assasin to kill Jay.

In the Upworld, Jay isn't doing well in school and considers dropping out. Meanwhile, in the Downworld, Fractal invents a helmet that allows kids to through the wall to the adult side, causing Jay & Flash to compete for the chance to test it.

In the Upworld, when Val starts dating a new man, Steve, Jay decides he doesn't like the man. Meanwhile, in the Downworld, Macro orders that all copies of ""The Fax"", a newsletter Alpha produces be stopped and the Bladers circulating them be eliminated.

In the Upworld, when Jay feels isolated at home he makes plans to run away and Steve promises Jay that he will search for Brad, despite Jay's claim that he doesn't want to be found. Meanwhile, in the Downworld, Fractal's new invention erases all Alpha's work and kills one of her assistants.

In the Upworld, Jay continues to see Sierra, despite warnings from Keith and Donna. Meanwhile, in the Downworld, Finger plans to stop the revolution by turning Jay's army against each other.

In the Upworld, Jay finally comes face-to-face with his father, Brad and learns the truth. Meanwhile in the Downworld, Jay prepares to take control of the tower, but Finger despersately tries to stop him.

In the Upworld, Keith puts up a poster in Jay's room of actress, Sierra Jones, which awakens Jay once again. In the Downworld, when Jay and Flash become lost in a maze of mirrors, Flash must face his inner demons while Jay must choose between both worlds.

In the Upworld, Val protests at the drugs used to sedate Jay as she learns that she must take the insurance company to court over Brad's policy. Meanwhile, in the Downworld, Fractal uses a new device to help Jay forget about Brad, but instead it causes a flashback to the day his father drowned.

In the Upworld, Val takes the insurance company to court and must testify that she believes Brad is dead. Meanwhile, in the Downworld when Jay meets the pirates again, they convince him to go inside a giant clock that transports him to a middle-world where his father is alive.

In the Downworld, while tracking Brad, Medea, Alpha, Jay & Flash go through the wall to the ""adult"" side and they are pursued by Iceface, who makes sure that adults stay on their side of the wall. Meanwhile, in the Upworld, Sierra organizes a benefit for Driftwood, and Arthur asks Val to attend as his date.