The Confusion ending is different from the other endings, because it's the only one where Stanley and the narrator aren't at odds with each other (at least, not completely). Instead, the narrator treats Stanley as a partner, and the two of them blunder their way forward, together—never really accomplishing anything, but still.
So how does this occur? To begin, Stanley enters the door on his right, and after admiring the employee office, he gets back on track, but only briefly, because he then goes down the elevator. After that, the Narrator tries to figure out which door out of six Stanley needs to enter. After going back on two decisions, he opens a garage door. After Stanley follows this path for a moment, he finds himself high above the monitor room. The Narrator regards this as a spoiler, and thus resets the game.
Stanley then attempts to proceed on his adventure like normal from the beginning, but when he gets to the two-door room, there are six doors now. Confused, the Narrator tells Stanley to wander around, hoping that they can find the story. After wandering around aimlessly for a moment, the Narrator gives up and tells Stanley he's resetting the game again, saying it can't get any worse than this.
But it did get worse, because this time, when Stanley gets to the two-door room, there aren't any doors. The Narrator tells Stanley to turn around, hoping the story is back there. After some Alien Geometries, Stanley hits a dead end, and turns around. When he does more turns than possible again, Stanley finds himself in what appears to be a rundown wooden house. The Narrator tries to figure things out again, and then just telling Stanley he won, but decides that's an empty victory, so he gets an idea and resets the game again.
This time, when Stanley leaves his office, the Narrator reveals his big idea: The Stanley Parable Adventure Line. Nothing could be simpler than following the Line, right? So after following the Line for a moment, the Narrator adds some adventurous music. Stanley walks the path of the Line for a long time, until eventually, the Narrator tells him to look at the Important Fern. After that, TSPAL crosses back over Its path in the second room, and then leads Stanley back to the high ledge above the monitor room again. Now this is still a spoiler, so the Narrator resets the game yet again.
Stanley reappears back in his office room again, with the Line outside his door again. Stanley begins following the Line, but the Narrator closes the door, saying that the Line never did anything for them. He then decides that him and Stanley should just create their own adventure instead, and opens another door. After even more Alien Geometries and aimless wandering, the Line busts through the ceiling and begins rambling about, but the Narrator simply tells him to ignore It. After some more walking, the two come to a set of two doors. This excites the Narrator, because they finally get to make a decision. The Narrator applies some Insane Troll Logic and figures out that they should enter the right door. They do, and discover the best part of the adventure: A board with the Confusion Ending events detailed out. The Narrator discovers that the game is still scheduled to reset a few more times, and some other events are supposed to play out. The Narrator, however, decides that he won't go through with it, which is apparently good enough to satisfy the board, as the clock stops after he asserts his refusal to continue. The Narrator begins to wonder what to do next, but the game does a hard reset with a loud noise, ending this story.