The Prologue section of Darkwood is the tutorial of the game. It begins with the player controlling The Doctor as he wakes up in his house from a dream. Exiting his study, and passing through the living room with two large cages and a strange, static-imbued radio, The Doctor collects his things and leaves, searching for a tractor which might contain some Gasoline.
Outside there is a pile of wood logs, a tied up dying dog, a ruined car (Referred to as "My 125p" by the Doctor, and containing The People's Tribune), a broken well, and an empty grave. Past the fence there is an axe and a pile of wood logs. From here on, the dog can be killed with the axe if the player chooses to, but this has no effect other than a dialogue change.
After learning how to attack by chopping a tree out of the way, the Doctor continues along the path and passes between several rocks and trees and a dead cow containing the Bone, as well as a paved road blocked by what appear to be large chunks of wooden roots (See Trivia). A torch is semi-necessary, in order to pass by an abandoned house containing several dead bodies, and a ritual area with strange markings and defiled, stitched corpses, both human and animal, as well as several scattered clothes.
The Doctor finds the Protagonist gravely wounded, and takes his key. A cinematic follows, showing the Doctor brought the Protagonist back to his house and intends to find out where the key leads to, possibly indicating it leads to the door out of the woods. It is heavily suggested the protagonist is drugged for interrogation, and as of Alpha 7, it has been confirmed that the Protagonist received a severe beating from the doctor, as well as death threats, should he not cooperate.
After this, the protagonist wakes up inside the Doctor's House, locked in the room with the trapdoor with some rags and wire, possibly in a dream sequence. Fashioning a lockpick to open the trapdoor, the protagonist finds the means to escape.
Breaking down the door, he catches a glimpse of the Doctor, and the lights immediately go out, the generator nearby having dried up. The player can then hear footsteps, and a person in the northern inaccessible room asks to be let out. The original office, where the Doctor awoke, appears to be missing.
The protagonist heads into the southern, previously inaccessible room, and finds a metal slab with leather straps (where he might have been tortured/drugged as a part of the interrogation), a Generator and a crate containing survival materials and a Dog Tag, replaced in the final release with a Plastic Chick. On the room with the radio, a strange man containing dials instead of eyes keeps muttering the password to the northern room. After unlocking the northern room and killing the man inside, who is presumably Janek, a relative of Chicken Lady, the house is attacked by several Black Chompers and the Prologue ends. The last thing seen before Chapter 1 starts is a short cinematic showing the Trader picking up and rescuing the Protagonist.
- As of Alpha 6, the Prologue appears to be undergoing active development. Recent versions have expanded the path that the Doctor takes before reaching the Protagonist, as well as adding new story items to investigate.
- Before Alpha 7, a body identical to the protagonist was strapped to the metal bed. Dialogue hinted it to be a wax dummy, and it would disappear after a while. The corpse now appears there once the player makes a return to this house, during Chapter 1.
- According to some dialogue lines added on Alpha 7, the forest that surrounds and forms Darkwood is said to be growing extremely fast, blocking all ways out of that place.
- Alpha 7 added a Player Map to the prologue, as well an expanding it. Alpha 7.1 brought further changes, notably on the starting cutscene's text.
- Notably, if one heads towards the door where Janek is locked, and remains around the house without opening that door for some time, the distorted man will disappear, having been re-replaced by the radio. This is one of many evidences that the Protagonist´s perception cannot be trusted at all times.
- Before Alpha 7, the dead cow appeared to be recently killed. Probably due to the fact that it made little sense for a fresh cow to yield only a bone, the animal was changed to a skeleton.