The jointer creates this 90 degree edge of a board by first flattening one face of the board and also squaring up the edge.
This is done by passing the board face along the surface of the machine starting on the in-feed table. The in-feed table is usually the part of the jointer that adjusts to determine the amount of material you are removing with each pass. From the in-feed table you slide board along and into the cutter.
Apply even pressure to the board and pass it over the rotating cutter. This will be a spindle with a few long knives or dozens of small square blades. (This cutter is very similar to the one utilized in the planer. This allows for the creation of combo machines that are jointer/planers and have two functions using the same blade.)
After passing over the blade the board then travels to the out-feed table. The out-feed table is set to the same height as the blade and you want to make sure to transfer pressure to the part of the board on the out-feed table to ensure a flat cut. This process is repeated until the face is flat and even.
Once this phase is complete, you place the new perfectly flat surface of the board against the vertical fence and rest one edge of the board on the in-feed table. You then pass this through the same direction and process as the flattening of the face but this time making sure to keep even pressure on the fence as well as the feed table surfaces. This will take multiple passes as well, but once you are finished you will have a board that the will be able to be processed through other machines and give you accurate, uniform results along the length of the board.