The Broken Seal is the location of the final colossus, Malus. The area gets its name from the seal placed on the gigantic stone door that previously blocked all entrance into it. To break the seal into the final location, the player must raise their sword to the light, and move the crosshair over the opening in the door. Doing so will trigger a short cutscene of the door opening, after which the area will be completely accessable. The Broken Seal is one of the only locations in the game that has a save shrine in close proximity to the colossus (the other being Misty Falls, which is located near Pelagia).

Upon entering The Broken Seal, the player will see a save shrine to the right, and a set of stairs to the left. The stairs lead upward to the one remaining bridge that leads to Malus' area. There are other bridges in this area, but many of them have crumbled away completely or to the point of being inaccessable.

The Broken Seal is the only location in Shadow of the Colossus in which the player will experience weather change and change in wind direction. The final battle with Malus takes place in a thunderstorm, and is the only instance other than the opening cutscene and the end credits in which rain and thunder are seen.