After crashing the jeep on the first level and proceeding, you will reach an area with a barricaded gate. Climb over the rocks and go in. After taking out the enemies, search for some boards over a small doorway off on one of the areas. Slice them up and enter to find the hatch on the ground near the back corner.
Go to the Alkali Lake section of the Frozen Tundra (before the Agent Zero fight) and find the fallen tree just past the long road section with the shield troops. Enter the forest that leads to a cave to find a sword and skeleton. Collect up the mutagen.
On the first level at the Gatecrasher objective, crash the jeep through the gates killing all enemies. To the left of the gate there is a boarded up door. Cut the boards down, and enter it to find the mysterious hatch.