Sellars reappears in the Atascos' virtual world and begs Renie and the others to flee into the network while he tries to hide their presence. They are to look for Paul Jonas, he tells them, a mysterious virtual prisoner Sellars has helped escape from the Brotherhood. Renie and company make their way onto the river and out of the Atascos' simulation, then through an electrical blue glow into the next simworld. Panicked and overwhelmed by too much input, Martine finally reveals her secret to Renie: she is blind.

Their boat has become a giant leaf. Overhead, a dragonfly the size of a fighter jet skims into view.

Back in the mountain fortress, in the real world, Jeremiah and Renie's father Long Joseph can only watch the silent V-tanks, wonder, and wait.

Paul Jonas still seems to be adrift in time and space. He has recovered most of his memory, but the last few years of his life remain a blank. He has no idea why he is being tossed from world to world, pursued by the two creatures he first knew as Finch and Mullet, and he still does not know the identity of the mysterious woman he keeps encountering, and who has appeared to him even in dreams.

He has survived a near-drowning only to find himself in the Ice Age, where he has fallen in with a tribe of Neandertals. The mystery woman appears to him in another dream, and tells him that to reach her he must find "a black mountain that reaches to the sky."

Not all of the cave dwellers welcome the unusual stranger; one picks a quarrel that results in Paul being abandoned in the frozen wilderness. He survives an attack by giant cave hyenas, but falls into the icy river once more.

Others are having just as difficult and painful a time as Paul, although they are better informed. Renie Sulaweyo originally had set out to solve the mystery of her brother Stephen's coma with her friend and former student !Xabbu, a Bushman from the Okavango Delta. With the help of a blind researcher named Martine Desroubins, they have found their way into Otherland, the world's biggest and strangest virtual reality network, constructed by a cabal of powerful men and women who call themselves The Grail Brotherhood. Summoned by the mysterious Mr. Sellars, Renie meets several others who have been affected by the Grail Brotherhood's machinations—Orlando Gardiner, a dying teenager, and his friend Sam Fredericks (who Orlando has only recently discovered is a girl), a woman named Florimel, a flamboyant character who calls himself Sweet William, a Chinese grandmother named Quan Li, and a sullen young man in futuristic armor who uses the handle T4b. But something has trapped them within the network, and the nine companions have been forced to flee from one virtual world to the next on a river of blue fire—a virtual path that leads through all the Otherland simulation worlds.

The newest simworld is much like the real world, except that Renie and her companions are less than a hundredth of their normal size. They are menaced by the local insects, as well as larger creatures like fish and birds, and the members of the group become separated. Renie and !Xabbu are rescued by scientists who are using the simulation to study insect life from an unusual perspective. The scientists soon discover that, like Renie and !Xabbu, they are trapped online. Renie and !Xabbu meet a strange man named Kunohara, who owns the bug world simulation, but claims he is not part of the Grail Brotherhood. Kunohara poses a pair of cryptic riddles to them, then vanishes. When a horde of (relatively gigantic) army ants attacks the research station, most of the scientists are killed and Renie and !Xabbu barely escape from a monstrous praying mantis.

As they flee back to the river in one of the researchers' aircraft, they see Orlando and Fredericks being swept down the river on a leaf. As they attempt to rescue them, Renie and !Xabbu are pulled through the river gateway with them, but the two groups wind up in different simulations.

Meanwhile, in the real world outside the network, other people are being drawn into the widening Otherland mystery. Olga Pirofsky, the host of a children's net show, begins to suffer from terrible headaches. She suspects that her online activities might have something to do with it, and in the course of investigating her problem, begins to learn of the apparently net-related illness that has struck so many children (including Renie's brother.) Olga's research also draws the attention of a lawyer named Catur Ramsey, who is investigating the illness on behalf of the parents both of Orlando and Fredericks, since in the real world both teenagers have been in a coma ever since their entrance into the Otherland network.

John Wulgaru, who calls himself Dread, and whose hobbies include serial murder, has been an effective if not one hundred percent loyal employee of the incredibly wealthy Felix Jongleur, the man who heads the Grail Brotherhood (and who spends most of his time in his Egyptian simulation, wearing the guise of the god Osiris.) But in the course of killing an ex-member of the Brotherhood at Jongleur's orders, Dread has discovered the existence of the Otherland network, and has even taken over one of the sims in Renie's marooned company. As his master Jongleur is caught up in the final arrangements for the Otherland network—whose true purpose is still known only to the Brotherhood—Dread busies himself with this new and fascinating puzzle. As a spy among Sellars' recruits, Dread is now traveling through the network and trying to discover its secrets. But unlike those in Sellars' ragtag group, Dread's life is not at risk: he can go offline whenever he wishes. He recruits a software specialist named Dulcie Anwin to help him run the puppet sim. Dulcie is fascinated by her boss, but unsettled by him, too, and begins to wonder if she is in deeper than she wants to be.

Meanwhile, a bit of Dread's past has surfaced. In Australia, a detective named Calliope Skouros is trying to solve a seemingly unexceptional murder. Some of the terrible things done to the victim's body are reminiscent of an Aboriginal myth-creature, the Woolagaroo. Detective Skouros becomes convinced that there is some strange relationship between Aboriginal myths and the young woman's death she is investigating.

Back in the Otherland network, Renie and !Xabbu find themselves in a weird, upside-down version of the Oz story, set in the dreary Kansas of the original tale's opening. The Otherland simulations seem to be breaking down, or at least growing increasingly chaotic. As Renie and !Xabbu try to escape the evil of Lion and Tinman—who seem to be two more versions of Paul Jonas' Finch and Mullet—they find a pair of unlikely allies, the young and naive Emily 22813 and a laconic gypsy named Azador. Emily later reveals that she is pregnant, and says Azador is the father. Separated from Azador during one of the increasingly frequent "system spasms," they escape Kansas, but to their surprise, Emily (who they had thought was software) travels with them to the next simulation.

Orlando and Fredericks have landed in a very strange world, a kitchen out of an ancient cartoon, populated by creatures sprung from package labels and silverware drawers. They help a cartoon Indian brave search for his stolen child, and after battling cartoon pirates and meeting both a prophetic sleeping woman and an inexplicable force—entities that are really Paul Jonas' mystery woman and the network's apparently sentient operating system, known as the Other—they escape the Kitchen and land in a simulation that seems to be ancient Egypt.

Meanwhile, their former companions, the blind woman Martine and the rest of the Sellars' recruits, have hiked out of the bug world to discover themselves in a simulation where the river is made not of water but air, and where the primitive inhabitants fly on wind currents and live in caves along vertical cliffs. Martine and the others name the place Aerodromia, and although they are nervous about trying it at first, they soon discover that they can fly, too. A group of natives invite them to stay in the tribal camp.