In s2-ep2 "Adrift", we first see the countdown clock in the hatch. After Kate and Locke had entered the hatch in s2-ep1 "Man of Science, Man of Faith", they encountered Desmond, a mysterious recluse who had been living in the hatch. Desmond approached the two of them with an assault rifle, demanding to know if Locke was "him". Desmond asked him, "What did one snowman say to the other snowman?", as an apparent password riddle for ensuring that Locke was indeed the person Desmond had been waiting for. When Locke was unable to give the proper answer, Desmond realized that Locke was not the "him" Desmond was waiting for. Desmond threw a rope to Kate and told her to tie Locke up, but Locke convinced him that Kate should be tied up instead. Locke tells Desmond that Kate is the more dangerous of the two of them, since she was a fugitive. Over Kate's protests, Locke ties her hands behind her back and secretly puts a knife into the back of her jeans, before locking her in a storage room.
Once Locke and Desmond were alone, they began questioning one another. Just after Locke tells Desmond that no members of the group have become ill, they hear a beeping noise and Desmond leads Locke into a computer room inside the hatch. Locke sees a countdown clock on the wall, with the numbers dropping from 2:38 to 2:37 to 2:36 as the beeping continues. Desmond forces Locke to enter the numbers 4 8 15 16 23 42 into the computer, and tells him to press the execute button. When Locke pushes the execute button, the countdown clock resets to 108:00. Just after the clock resets, Jack enters the hatch looking for Locke and Kate. Wary of danger, Jack calls out to them. Desmond presses his gun to Locke's head as he approaches Jack, who is also armed. Desmond fires a warning shot as he tells Jack to drop his weapon and the shot nearly hits Kate, who is hiding in an air vent overlooking the room.
In s2-ep3 "Orientation", Kate jumps down into the gun vault from the air vent and grabs a shotgun before moving up behind Desmond and hitting him in the back with it. As he falls, his weapon discharges and accidentally shoots the computer, leaving it smoking. Jack holds him down as Desmond begins to wail, saying "What did you do? What did you do? We're all going to die. We're all going to die." Desmond struggles to get up and tells Jack to look at the wall, and explains that it is a timer that is counting down. He says he has to enter the code and push the button, and that he needs to fix the computer. While trying to fix it, Desmond tells Jack and Locke that Kelvin, who had brought him into the hatch after his sailboat crashed on the island 3 years earlier, told him that entering the numbers and pressing execute would save the world. He directs Jack and Locke to watch the orientation film hidden in the living quarters of the hatch. They watch the film and hear Dr. Marvin Kandle say that the code must be input every 108 minutes, when the alarm begins to sound. When Desmond is unable to fix the computer, he panics and flees the hatch, disappearing into the jungle after giving Jack the code to be entered.
Sayid is able to fix the computer and Locke enters the numbers as the countdown timer begins to sound, and Jack returns in time to hit the execute button at Locke's insistence. Locke then organizes the survivors into shifts to make sure that the numbers are entered when the alarm begins to sound.
In s2-ep14 "One of Them", Locke is in the hatch when Sayid enters with Henry Gale, who had been shot through the shoulder by Danielle after being taken prisoner. Jack enters and treats Gale’s injuries while Locke and Sayid quietly discuss the possibility that Gale may be an Other. Sayid tells Locke that he must find out the truth of who he is, and that he needs privacy to do it. Locke agrees to change the combination on the armory door for Sayid.
While Sayid is interrogating Gale inside the armory, Jack becomes angry when he realizes Sayid has taken the pliers to torture Gale and demands that Locke open the door. When Locke refuses, the alarm begins to sound and Jack tells Locke that if he does not open the door, Jack will not allow Locke to enter the code into the computer. Locke finally rushes to open the armory door and then runs to the computer, frantically entering in the numbers. He makes a mistake in his haste and has to backspace, wasting valuable seconds, and the countdown timer hits zero. The tiles begin spinning around and reveal black and red tiles with hieroglyphics on them and a sound is heard that has been described as the sound of machinery starting up. Four of the tiles lock into place as Locke enters the last number and hits execute before the final tile locks into place. The timer resets to 108:00 and the sound of machinery winding down is heard.
The symbols shown on the tiles have been translated to read Causitive Die, or Cause To Die. It is unknown what this means, or if the countdown had been stopped when Locke was able to hit execute before the final tile locked into place.
