The vault is divided into two sections, with a large wall separating them. The only way through is by a large gate in the wall or by one of the smaller barred windows in the wall, all of which are closed. They are opened when Drake stands in a wooden elevator, which drops down, acting as a counterweight and pulling the window or gate open. In the game, Drake opens one of the windows, before climbing through and opening the main gate from the other side, allowing Elena to pass through.
The first section of the vault is navigated by following the roman numerals on the corner of Francis Drake's Map. There are metal plates in the ground, each of which has a numeral on it, pointing in different directions, with only the numerals II, V and VII pointing in the right direction. The first section of the vault contains a defence system against intruders, a set of large, swinging torches that will knock Drake off the narrow walkways to his death below.
This is a room towards the top of the vault where the treasure was hidden, but when Nate and Elena arrive it is already gone, taken by the Germans years ago. The Heart of the Vault, however is the final resting place of Francis Drake, as Nate and Elena find his body there. This is also where Nate first encounters The Descendants. There are two exits from The Heart of the Vault, one leading back to the main vault, and another leading to the German Submarine Bunker.