- "All units. This is Sergeant Kelly. We're under attack by an unknown enemy force! Fall back to Marine HQ to regroup!"
- ― Sergeant Kelly [src]
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 (Marine HQ). Though he appears to be somewhat cold, he is very well respected for his duties and leadership. A career military man, he only expects the best from his men. He gets 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 very obvious when you first encounter him, as the first thing he says to you is: "Took your sweet time, marine?"
Fortunately, it's your first day so he shrugs it off and gives you your first assignment (allowing you no time to settle in due to the 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 safely back to HQ. Sergeant Kelly then sends you on your way with a Sentry Bot to guide you (he remarks that he hopes you follow the Sentry better than you've followed orders so far).
Not long after you locate the missing scientist, the demonic outbreak occurs killing (and possessing) Dr. Ishii and 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. His role in the game is significant: as he commands the Doomguy with orders different than those from Councilor Swann, he creates a conflict as to what the Doomguy should do. The question is whether or not to alert the fleet of the situation: Kelly wants reinforcements, Swann fears that the hordes of Hell will use it to invade Earth. In any case, it doesn't really matter, since if the Doomguy doesn't contact the fleet, then Betruger does it himself.
After sending/canceling the transmission, the player is not contacted by Kelly again until he reaches Delta Labs. Kelly appears on a monitor in a recorded message and tells the player to meet him at Service Tunnel 1, but when the player gets there, Kelly is nowhere to be found (in fact, a trio of Cacodemons teleports in). After this, the player does not see or hear from Kelly again until the CPU Complex.
Although Kelly doesn't appear in Resurrection of Evil, his office can be found, where he kept a double-barreled shotgun. Interestingly, there is a picture of him killing a bear with his shotgun, as well as having the trophy of the same bear mounted on his wall.
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. The player encounters the wounded Swann, who warns him that Kelly has been turned. The player makes his way to the CPU complex where he 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 and taunts him saying: "I killed that pathetic bodyguard, and now I shall 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 Kelly's "incident" still remains uncertain. Some affirm 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, maybe knowing it would be taken over by the demons). However, a careful review of Master Sergeant Kelly's radio dialogue from the start of the invasion until the player reaches the comm tower strongly suggests he was never initially in league with Betruger:
His statements and orders were concurrent with his command leadership experience, despite extremely limited intel on the opposing enemy forces. From Kelly's standpoint, he was dealing with a completely unprecedented full attack. Nothing was known about their numbers and capabilities. All that was known to him amid the confusion, was that he was quickly losing men, the units were cutoff from one another and unable to regroup or fortify their positions, and most the base was already in enemy hands. As more units fell, Kelly realized he needed reinforcements if they had any chances of survival. Bravo Team reached Marine HQ (before the player) where Kelly assumed they were the last combat operational fireteam. When he realized the player survived, he commends him and sends him to link up with Bravo. Kelly urgently needed the reinforcements and ordered the signal sent; while Swann's disagreed on the basis off not knowing what they were up against, and keeping the threat quarantined to Mars until then. Had Kelly and Betruger had been allies, he would have been in position to send the distress call to Earth the instant the invasion began. Furthermore, Kelly would have no reason for being in league with Betruger before the invasion, since he never made a trip into Hell.
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 seems surprised that the player is still alive. He also speaks in a somewhat cryptic tone, rather than exhibiting his usual military-mannerism. This suggests that some alteration has occurred to him by that point in the game. It should also be noted that if the player chooses not to contact the fleet back at the Communications Facility, Kelly will angrily start to order the player to send the transmission only to be inexplicably cut off. This might be the point at which Kelly was attacked and converted over to Betruger's side. Another explanation is that he might have been converted when Betruger tells the player "Your friends are with me now, and soon you will join them" in the garage of delta labs sector 1, or that could be when swann got fatally wounded by Kelly.
- If the player uses a cheat code for all weapons, the player can kill Sarge in the control room, even though this won't mean that Sarge doesn't appear later.
- in the BFG edition, Kelly has brown hair
- In the French version of Doom 3, Sarge's "final warning" is in English.