Master Sergeant Thomas Kelly is one of the first characters the player meets in Doom 3. He is at the top of the enlisted chain of command on the Mars Base at Marine HQ. Though he appears to be somewhat cold, he is well respected for his duties and leadership. A career military man, he only expects the best from his men. He is easily agitated when one slacks on his efforts, and typically assigns slacking marines to the worst duties as punishment (such as being assigned to the solid waste facility). Kelly makes this clear when you first encounter him, as the first thing he says to you is, "Took your sweet time, marine?"
Fortunately, it is your first day so he shrugs it off. Referring to you as the "ranking FNG," he gives you your first assignment immediately, allowing you no time to settle in due to the ongoing lack of troops. You must locate a scientist who is missing and never showed to his post (Dr. Ishii, Delta Labs researcher) and bring him back safely to HQ. Sergeant Kelly then sends you on your way with a sentry bot to guide you, remarking that he hopes you can follow the sentry better than you have followed orders so far.
Not long after you locate the missing scientist, the demonic invasion of the base occurs, killing and possessing Dr. Ishii along with almost everyone on the entire base. Sergeant Kelly, now in Delta Labs, orders all remaining marines to head back to HQ for further orders. You are the only marine to arrive at HQ alive.
When you approach the communications monitor, Sergeant Kelly appears on the screen. He seems both surprised and relieved to see you and gives you your next set of orders: Link up with Bravo Team in order to send a distress call to the Earth fleet for backup. His role in the game is significant: as he commands the Doomguy with orders in opposition to the goals of Counselor Swann, he creates a conflict as to what the Doomguy should do. This culminates in a choice given to the player in the Communications facility to either send Kelly's message to the fleet, or to follow Swann's urgings to discard the message due to the risk it could pose if the fleet were overwhelmed by the demons, leaving their ships available for use.
If the player chooses to send the transmission, he is praised by Kelly and berated by Swann, and Kelly will tell the player to meet him in Delta. If he cancels the transmission, Swann will ask the player to meet up with him and Jack Campbell at the monorail station, while Kelly angrily orders the player to send the message several times until his radio is abruptly cut off by unknown interference. Regardless of the choice made, however, Dr. Malcolm Betruger will intervene - if the transmission is canceled by the marine, he will send one himself.
After sending or canceling the transmission, the player is not contacted by Kelly again until he reaches Delta Labs. Kelly appears in a video link-up message on a monitor in the power distribution grid control room and tells the player that the Delta Complex has been compromised and to meet him at Service Tunnel 1. However, when the player arrives there, Kelly is nowhere to be found - in fact, a trio of cacodemons teleports in. After this, the player will neither see nor hear from Kelly again until he reaches the CPU Complex.
At some point during the game, Kelly is converted over to the demons' side. He ambushes Campbell and Swann in Delta Labs, gravely injuring Swann. Campbell chases after him, leaving Swann behind at the man's request. The player encounters the wounded Swann, who warns him that Kelly has been turned. The player makes his way to the CPU complex where demonic spirits constantly taunt him with messages such as "Sarge is waiting for you," and "Sarge is gonna kill you!" He eventually finds Campbell, who has been ambushed and mortally wounded by Kelly. Before expiring, Campbell tells the player that Kelly has his gun. At this point, Kelly contacts the player telepathically and taunts him, saying, "I killed that pathetic bodyguard, and now I'll kill you."
In the next level, the player comes face-to-face with Kelly, who has been transformed into a hideous tank-like monstrosity called Sabaoth. The player has no choice but to fight and kill his former commanding officer. After you defeat Sabaoth, you are rewarded with Campbell's BFG 9000.
The reason for and timing of Kelly's corruption remains deliberately vague. It is equally possible to believe that he was working with Betruger and the demons since the beginning (substantiated by the fact that he insisted in contacting the Earth armada to bring them to Mars, possibly knowing that it would be taken over by the demons), or that he was captured, brainwashed, and transformed by Betruger to serve him, and that his zealous attempts at contacting the fleet to obtain reinforcements were simply based on prudent military logic (realizing that the battle is lost without reinforcements).
It should be noted that Kelly's appearance and behavior are subtly different once the player reaches Delta Labs. His eyes appear glazed over and he speaks in a rather cryptic tone, instead of exhibiting his usual military mannerisms. This suggests that some alteration has occurred to him already by that point in the game. It must also be noted that the abrupt inexplicable cut-off of Kelly's angry orders to the player to send the transmission if it is canceled at the communication facility, and his radio silence afterward, suggest this as a possible point at which Kelly was attacked and converted over to Betruger's side.
- The character Sarge of the Doom movie (played by Dwayne "The Rock" Johnson) is partially based on the character of Sergeant Kelly.
- If the player uses a cheat code for all weapons, the player can kill Sarge in the control room, even though this will not affect Sarge's later appearances or actions.
- The Resurrection of Evil expansion reveals that Kelly had a personal office in the Erebus Facility, and that he was a bear hunter on Earth during his times on leave. A portrait of him with one of his kills can be seen hanging on the wall next to his prized double-barreled shotgun. A nearby video game in the office named Sarge's Big Game Hunt seems to pay tribute to him as well.
- In the French version of Doom 3, Sarge's "final warning" is in English.