Tomb Raider: Underworld is a single-player action-adventure game where the player controls the protagonist, Lara Croft, from a third-person perspective, through a variety of locations around the world.  Lara can jump, climb and shimmy along ledges and vertical poles or ladders, crawl through small spaces, and swing on ropes and horizontal poles. Some areas have climbable surfaces she can scale, and some ledges allow her to stand on them and shimmey along. Other abilities include wall jumping between two adjascent surfaces, interacting with objects and switches, using a grappling hook to latch onto special rings for both puzzle solving and environmental traversal, and swim and dive underwater for a limited time. Different button combinations can create more moves such as a roll and swan dive. Puzzles revolve around Lara finding keys to mechanisms in the environment, or manipulating different mechanisms to trigger larger elements within and around the environment. There are also traps which need to be avoided, some of them involved in the puzzle design. During some levels, Lara has access to an all-terrain bike which is used in both navigation and puzzle solving.

During combat, Lara automatically locks on to enemies and fires with her equipped gun, with the player able to switch to another target within range and move freely to avoid enemy attacks. When using two weapons, she is able to target up to two enemies at once. Through most of the game Lara has access to seven weapons, selectable from the main menu; her default twin pistols with infinite ammunition, and a shotgun, submachine guns, assault rifle, speargun, tranquillizer gun, and sticky grenades all with limited ammunition. During the last two levels, Lara also has access to the magical artefact Mjolnir, which instantly kills most enemies. Lara's health is represented by a coloured figure, with the game resetting to a checkpoint if she dies; medipacks and artefact collectables heal her, and hard-to-reach relics collected through the game raise her health cap. The difficulty setting can be tailored, with puzzle, combat and platforming difficulties each having sliders influencing their respective challenge in-game. There is also an option on Lara's PDA to receive tips about navigation or solving puzzles. A sonar map is accessible through the PDA, showing a generated 3D representation of Lara's environment.

The PlayStation 2 and Wii versions are generally similar to other versions, but with smaller environments and puzzle structure due to hardware limitations; the Wii version also incorporates dedicated combat controls and puzzles revoling around the motion controls. The Nintendo DS (DS) is a two-dimensional (2D) side-scrolling platformer, with Lara navigating self-contained areas while progressing through each level. There are two mobile versions with differing gameplay styles; one is a 2D side-scrolling platformer similar to earlier mobile Tomb Raider games, while the other uses 3D graphics and incorporates platforming and combat elements similar to the home console versions though Lara is restricted to moving forward or backward and some movements are automatic triggered using button prompts.

The story begins in medias res; Lara Croft navigates her home Croft Manor after an explosion, then is shot at by her tech assistant Zip. One week earlier, Lara is investigating a sunken island in the Mediterranean Sea as part of her search for Avalon, hoping it will lead her to an explanation for the disappearance of her mother Amelia and salvage her father Richard's academic reputation despite the scepticism of Zip and her research assistant Alister. The island houses ruins dubbed "Niflheim", one of the many Norse underworlds, and Lara discovers one of the gauntlets attributed to the god Thor to wield Mjolnir. While ambushed by mercenaries sent by rival Amanda Evert, Lara recovers the gauntlet, which has shaped itself to her hand. On Amanda's ship she also meets an imprisoned Jacqueline Natla, former ruler of Atlantis presumed dead after their last encounter. Natla reveals that Amelia was sent to "Helhiem"−another name for Avalon−and directs Lara to ruins in Thailand, hinting that her father also searched for Mjolnir before she is taken by Amanda as the ship sinks due to an explosion caused by the mercenary leader who ambushed Lara.

In Thailand, Lara navigates the ruins of "Bhogavati" and finds more ancient ruins that housed a gauntlet; Richard was sent there by Natla, but removed the gauntlet and destroyed a map showing the location of Thor's relics. From the use of his initials referencing her grandfather, Lara deduces that Richard hid the gauntlet in Croft Manor. Finding Richard's study in Croft Manor's catacombs, Lara finds the gauntlet and a tape-recorded message from Richard, revealing Helheim contained a powerful weapon and that he destroyed the map after recording it to prevent its use. She also encounters a pair of Thralls, undead guardians of Thor's relics created from eitr. Croft Manor is bombed, and Lara learns from Zip that the bomber, who looked identical to her, stole the magical stone Amanda used during Legend. Lara then encounters a Doppelgänger—a being modelled to look like Lara—who shoots Alister and flees; despite Zip's protests, Lara continues her quest so she can use Mjolnir to kill Natla. In the ruins of "Xibalba" in Mexico, Lara finds both Thor's belt−which powers the gauntlets and is protected by more Thralls−and ancient carvings detailing the myth of Jörmungandr, who will flood the world before fighting Thor, with both dying. In the ruin of "Valhalla" on Jan Mayen, Lara recovers Mjolnir, then confronts Natla.

Natla provides Lara with the coordinates of Helheim, but points out that only she knows the ritual to prepare its gates, so Lara reluctantly strikes a bargain and frees her from her cell. Amanda attempts to stop her, but the Doppelgänger attacks and apparently kills Amanda. Lara dives to the ruins of Helheim under the Arctic Sea, and with Natla's preparation opens its entrance with Mjolnir. Lara then discovers Amelia is turned into a Thrall and is forced to shoot her. Natla appears and reveals that she killed Richard after his betrayal in Thailand, then sets the Doppelgänger on Lara before leaving to awaken Jörmungandr, revealed as a metaphor for the Earth's faultlines; Natla intends to activate an ancient device above the faultlines' weakpoint and trigger apocalyptic volcanic activity. Amanda appears and apparently throws the Doppelgänger to its death, allying with Lara to stop Natla's plan. Lara finds the device and destabilises it, then throws Mjolnir at Natla, knocking her into a lake of eitr. Lara and Amanda then use the chamber's dais travel device, escaping to the Nepalese monastery where Amelia first disappeared. Amanda tries to restart their fight, but backs down and leaves when Lara refuses; before she leaves, Lara bids goodbye to her mother.

The downloadable content episodes "Beneath the Ashes" and "Lara's Shadow" are set after these events. The Doppelgänger, revealed to have survived, finds a disfigured Natla and is compelled through the magical command "Okh Eshivar" to take her to the Doppelgänger's birthplace in an ancient ruin. After the Doppelgänger restores the ruin's healing technology, Natla orders the Doppelgänger to kill Lara then itself. At Croft Manor, Lara finds notes on a Thrall-creating stone carved with the "Okh Eshivar" command. After a Thrall attacks from a cavern, she descends deeper into the catacombs and finds the stone. The Doppelgänger and attacks, and Lara says "Okh Eshivar" bringing the Doppelgänger under her control. After Lara questions the Doppelgänger's nature and the Doppelgänger states that they are both driven by something beyond their control−compulsion for the Doppelgänger and obsession for Lara−Lara frees the Doppelgänger from all commands and sends it back to Natla as a means of avenging Alister. Back at the ruin, the Doppelgänger destroys the device, then watches as a trapped Natla is drowned in a rising pool of eitr.