Joey Steward, now going by the name Steward only, begins his service to the Slender Man by getting his childhood memories taken away by The Blind Man. He then attends a meeting of Fears, meets Charlotte, a doll of The Wooden Girl, and afterwards gets his first assignment: to observe a woman being stalked by the Slender Man who shows no sign of the Compulsion. Steward is joined by Glorious and Acedia, two Revenants.
Steward can't figure out why she is not affected by the Compulsion, so eventually she is taken and tortured, then made into a proxy. He is given another assignment to figure out who is killing proxies; he is tipped of by a Camper that it is a magician named Sleight. Sleight ends up joining up with Maxwell, a former Lonely Hearts operative, who has stolen an important pocketwatch, which turns out to be the larval form of a Fear. Steward and the others chase him to Hope Township, New Jesery, and eventually end up in the "Land of Make Believe," an amusement park, where Maxwell tries to use the pocketwatch, but it merely sinks into his flesh and from his body is born The Manufactured Newborn. Numerous other Fears arrive to witness its birth.
Steward sees Sleight escaping and follows him into The Empty City. He finds Sleight, who doesn't know why he killed those proxies. Sleight shoots Joey and escapes. Later on, Steward finds Sleight again and again follows him into the Empty City - and this time, Sleight tells Steward about being followed and judged by an eye. Then the Empty City appears to kill Sleight.
Steward doesn't believe Sleight about the Eye until he starts seeing it himself. Then a runner named Spike starts targeting Steward and other proxies. Steward is given a vacation and he meets another proxy named Lexi, whom he starts to like. The vacation is cut short, however, when the killings begin again, but this time it is the work of Spike. Steward is kidnapped by Spike and another servant nicknamed Scarneck. Eventually, Lexi and the others find him in a densely wooded area and rescue him, but he tries to kill them and has to be tied up for 24 hours until the Compulsion wears off.
The Camper visits Steward again and gives him a hint about what is actually behind all of these events. Spike kills Glorious and Acedia and Steward kills him, but Scarneck kills Lexi. Steward kills her, but ends up distraught. Finally, he figures out who is behind it all: The Rake. It was his whispers that compelled Sleight, Spike, and Scarneck to kill and he took an interest in Steward since before, when he was being hunted by the Archangel.
Steward goes to a confrontation between the Slender Man and the Rake. However, it turns out that the Slender Man is just going to give Steward over to the Rake. This exchange is interrupted by the Wooden Girl who attacks the Slender Man. The Slender Man manages to burn her body, but she emerges from Charlotte's body. In the confusion of the battle, Steward runs away.
Now on the run, Steward finds that he is being targeted not only by the Slender Man, the Rake, and the Wooden Girl, but also by EAT. He has been infected with the Ichor and it won't be long now before he is a stage one Camper. He tries to get to the Empty City, but finds that the Eye and Judgment (in the form of Sleight's body) are waiting for him.
Now stuck in his apartment, with the Slender Man, the Rake, the Wooden Girl, EAT, the Eye, and even the Choir targeting him, Joseph Steward decides to go out fighting. He apologizes for all the bad things that he has done and tells all the monsters to come and get him.
- Hidden in the Trees introduced several new Fears and elements that were subsequently incorporated into the Mythos. It was the first appearance of the Blind Man, the Manufactured Newborn, and the Eye and introduced the concept of The Great Game.