Doom 3 is a story-driven action game played from a First-Person perspective. As with previous Doom games, the main objective is to successfully pass through its levels, defeating a variety of enemy characters intent on killing the player. Doom 3's more story-centred approach, however, means that the player often encounters friendly NPCs, who provide key plot information, objectives and inventory items. The game incorporates ten weapons for the player's use to survive, including conventional firearms and explosives such as a the Sub-machine gun, Shotgun and Shotgun, experimental plasma weaponry, and the traditional BFG 9000 weapon of the Doom franchise. Enemies come in multiple forms and with different abilities and tactics, but fall into two broad categories of either Zombies or Demons. Zombies are humans possessed by demonic forces, who attack the player's character using their hands and melee weapons or a variety of firearms, while demons are creatures from Hell, most of which attack using claws and spines, or by summoning plasma-based fireballs. The corpses of demons are reduced to ashes after death, leaving no trace of their body behind.
The game's levels are fairly linear in nature and incorporate several horror elements, the most prominent of which is darkness. This design choice is not only intended to foster feelings of apprehension and fear within the player, but also to create a more threatening game environment in which the player is less likely to see attacking enemies. This aspect is further enhanced by the fact that the player must choose between holding a weapon and holding the flashlight (until the BFG editions released in 2012 made the "duct tape mod" a standard feature), forcing the player to choose between being able to see and having a readied weapon upon entering a room, which consequently leads to a more deliberate pace for the player. In addition, the levels are regularly strewn with corpses, dismembered body parts and blood, sometimes used in conjunction with the game's lighting to disorient the player.
Frequent radio transmissions through the player's communications device also add to the atmosphere, by broadcasting certain sounds and messages from non-player characters meant to unsettle the player. Early in the game, during and directly after the event that plunges the base into chaos, the player often hears the sounds of fighting, screaming and dying through their radio transmitter. The ambient sound is extended to the base itself through such things as hissing pipes, footsteps, and occasional jarringly loud noises from machinery or other sources. Often ambient sounds can be heard that resemble deep breathing, unexplained voices,maniacal laughther and demonic taunting from the game's antagonists.
Early in the game, the player is provided with a PDA. PDAs contain security clearance levels, allowing the player to access certain areas that are otherwise locked and off-limits. Additionally, the PDA can be used to read e-mails and play videos that the player's character acquires during the game. Whenever the player picks up any of the other PDAs found throughout the game, its contents are automatically downloaded to the player's own device. Other PDAs often contain e-mails and audio logs for other characters, which can provide useful information such as storage or door key codes, as well as significant plot details.
The story of Doom 3 is conveyed through in-game dialogue and cut scenes, as well as E-Mails, audio logs and video files found throughout the game. The game opens with Elliott Swann and Jack Campbell arriving at Mars City, the main access to the UAC's Mars base, disembarking from an Earth transport, with the player's anonymous Marine just behind them. Swann and Campbell have a heated conference meeting with Dr. Malcolm Betruger as the first part of investigating the incidents and complaints about the facility while the marine heads to Master Sergeant Thomas Kelly for orders. Kelly gives the marine instructions to find a scientist from the Delta Labs who has gone missing. The marine finds the scientist in a nearby decommissioned communications facility, where he is frantically trying to send a warning to the UAC on Earth about Betruger's teleportation experiments. However, as he tries to explain the situation to the marine, another teleportation test takes place and loses containment, at which point the entire Mars base is swept with an unnatural shockwave, transforming most of the base's personnel into zombies as the forces of Hell invade through the teleporter's portal. Much of Doom 3, such as this section in the Delta Labs, was planned using storyboardsNow forced to fend off attacks from zombified base personnel and the Demons from Hell, the marine returns to Mars City, where Kelly remotely gives the marine orders to link up with another squad of marines (Bravo Team) and get a transmission card containing a distress call to the main communications facility to call for reinforcements. As the marine progresses through the base, he learns that Swann and Campbell have survived, and are also en route to the communications facility to prevent any messages being sent in hope of containing the situation on Mars. The marine squad is ambushed by demons and slaughtered in the EnPro Plant, and although the marine recovers the transmission card, he is too late to prevent the bulk of equipment at the communications facility being destroyed by Campbell. Kelly, however, directs the marine to a backup system, where the marine is given the choice of whether to obey Kelly's orders to send for reinforcements, or accept Swann's argument to keep Mars isolated until the exact nature of the invasion is understood, so as not to endanger Earth.The marine is told to go to the Delta Labs by Kelly or Swann, depending on whether the transmission is sent or not.
On the way to the Delta Labs, the marine is contacted by Betruger, who is now clearly shown to be working in cooperation with Hell in order to invade Earth. If the marine did not send the distress call to Earth, Betruger does so himself, hoping to use the ships bringing reinforcements to transport the demons to Earth. Betruger then unsuccessfully attempts to kill the marine using the toxic gases in the base's recycling facilities. Upon arriving at the Delta Labs, the marine learns of the details behind the teleportation experiments, expeditions into Hell to retrieve specimens and Betruger's increasing obsession with the tests, as well as of an archeological dig under the surface of Mars. The dig is excavating the ruins of an ancient civilization discovered on Mars, and has produced a relic known as the Soul Cube. According to a scientist the marine finds alive in the labs, the Soul Cube is a weapon created by the ancient civilization to defend against the forces of Hell. The scientist also reveals that the invasion began when Betruger took the Soul Cube into the portal at the beginning of the game, depositing it in Hell. The marine pursues Betruger through the labs, but is pulled into the main teleportation portal after being lured into a trap by Betruger.
The portal takes the marine directly into Hell, where he proceeds to fight his way through the large number of demons to the Soul Cube, defeating its demonic guardian. The marine is then able to reinitialize the teleportation equipment left by research expeditions into Hell and return to the Delta Labs. Betruger, however, tells the marine that although the main UAC teleporter has been destroyed, Hell is opening a Hellmouth on Mars, capable of bringing millions of demons to Mars. Further in the Delta Labs, the marine encounters the injured Swann. Swann informs the marine that Kelly has been working with Hell for possibly the whole time, and has been transformed by the demons. Telling the marine that Campbell has gone after Kelly, Swann gives the marine his PDA containing information on the location on the Hellmouth under the surface of Mars and assures him that he will try to make his way out of the base alone.
However, when the marine catches up with Campbell in the central computer processing sector of the base, Campbell is mortally wounded and only has enough strength to say that Kelly has taken Campbell's BFG 9000 weapon before expiring. Kelly then begins to taunt the marine in a demonic voice. The marine eventually faces off with Kelly in the central computer core, revealing Kelly as a cybernetic human grafted onto a tank-like base. The marine is able to kill Kelly and takes the BFG 9000 before proceeding deeper under the Martian surface to Site 3, the archaeological dig site where the Soul Cube was unearthed. At the primary excavation site, the marine discovers the Hellmouth, defended by Hell's mightiest warrior, the CyberDemon. Using the Soul Cube, the marine defeats the Cyberdemon in combat, and the Soul Cube then seals the Hellmouth. The ending cut scene shows the reinforcements from Earth arriving at the base to discover the carnage. They find the marine alive, but discover that Swann has died. They are, however, unable to locate Betruger, who in the final scene is shown in Hell, reincarnated as a dragon-like demon.