Tomb Raider: Underworld begins with Lara Croft's mansion exploding and being engulfed in flames. The game then rewinds back in time to a week before the explosion, just after the events of Tomb Raider: Legend. Lara is searching for Avalon, hoping it will lead her to an explanation for the disappearance of her long lost mother. Underneath the Mediterranean Sea, Lara discovers an ancient temple designating itself as "Niflheim", one of the many Norse underworlds. Deep within, she recovers one of Thor's gauntlets, after a lengthy battle with Amanda Evert's mercenaries and an encounter with an imprisoned Jacqueline Natla, on Amanda's ship. Natla tells Lara that the Norse underworld, Helheim and Avalon are one and the same and that she will need to find Thor's Hammer to open the Underworld and find her mother. Lara soon discovers that she will have to find Thor's other gauntlet and his belt if she wants to find and wield the hammer. Natla provides Lara with a starting point for her search in this quest – coastal Thailand. In Thailand, Lara doesn't locate the next gauntlet, but she finds evidence that her father had found it there and removed it before he died. She also discovers a message that reveals that her father and Natla had been working together at some point and that the relationship had not ended well. Lara is able to deduce where her father hid the missing gauntlet.
Back at the Croft Manor, Lara finds her father's secret office buried beneath her home. Upon his desk, Lara discovers the gauntlet as well as a tape-recorded message, warning her that Helhiem contains a powerful weapon. Suddenly, an explosion occurs and Lara's home becomes engulfed in flames, leading back to the opening events of the game. Zip tries to shoot Lara and claims that "Lara" detonated the bomb. When Lara returns to the burning office to recover the security footage, she encounters her doppelgänger who kills Alister Fletcher. After his emotional death, Lara resolves to continue with her quest. In Mexico, Lara finds both Thor's Belt and some ancient pictographs linking the weapon in Helheim to Jörmungandr, a mythical Norse sea-serpent, brought about by the seventh age. Her next stop are ruins on Jan Mayen Island that correlate to Valhalla. It is here that Lara finally recovers Thor's Hammer. In the meantime, Zip has managed to track Amanda down to a sister-ship of the one Lara sank earlier. Armed with Mjolnir, Lara boards the vessel and interrogates Natla once again. Natla provides Lara with the coordinates of Helheim, but points out that Lara does not know the Ritual of Odin, which is needed to open its gates, so Lara reluctantly strikes a bargain with Natla and frees her from her cell.
Lara travels to Egypt, and successfully retrieves the third piece of the Scion. After assembling all three pieces, Lara's earlier vision becomes much clearer. In Lara's visions two of the three Kings, Tihocan and Qualopec, are sentencing the third one, revealed to be Natla, to imprisonment. Natla, after releasing Atlantis' own army against itself in an attempt to bring about what she refers to as the Seventh Age, is imprisoned in the crystalline structure for a thousand years..
They rendezvous in the outer chambers of the Helheim complex, deep below the Arctic Sea. With the ritual performed, Lara is able to use Mjolnir to open the gates of Helheim. Along the way, Lara discovers the horrifying truth of her mother's fate – she has been turned into a thrall, thus Lara forcibly shoots her. Natla reveals the true extent of her manipulation of Lara, also revealing that she was the one who killed Lara's father. Natla goes, leaving the doppelgänger to kill Lara, but Lara is saved by Amanda. It is revealed that the Midgard Serpent was a Norse metaphor for the many tectonic divisions that encircle the world, beneath the seas. The doomsday device was built upon the most unstable junction of these lines and its activation would cause massive volcanic activity across the whole planet and the destruction of most of humanity. Lara successfully destabilises the device and strikes Natla with Mjolnir, sending her down into the pool of deadly eitr below. Lara and Amanda escape together using the dais, like the one that brought Lara's mother to Helheim, teleporting back to the temple in Nepal (from Tomb Raider: Legend).
Troels Brun Folmann composed the main theme of the game, and was the music supervisor for Underworld while Colin O'Malley was scoring the bulk of the music. Underworld's music is purely orchestral in style. There are pieces that do not loop, meaning they will only play one time and will be triggered on specific events. The score is made more of musical fragments, similar to the first five games of the Tomb Raider series, and there is less constant music than in Legend. In addition to gameplay music, Underworld's theatrical trailer also uses orchestral music. The featured piece is the 3rd movement: Lacrimosa, from Mozart's Requiem in D minor.
Beneath the Ashes as in the main game, the player controls Lara during Beneath the Ashes. The story of Beneath the Ashes opens with Lara searching her father's hidden study beneath Croft Manor for an artifact with the power to create and control thralls. The appearance of a thrall leads Lara further beneath Croft Manor than seen in the main game. Upon finding the artifact, Lara uses the phrase carved into it, "Okh Eshivar", to gain control over a thrall. The doppelgänger suddenly appears and charges towards Lara. Lara orders the thrall to "kill", but the doppelgänger easily destroys it. Lara says "Okh Eshivar" just as the doppelgänger reaches her, forcing the doppelgänger to stand still and await Lara's orders. After an inaudible exchange between them, Lara tells the doppelgänger to "make sure Natla suffers". Beneath the Ashes ends as the doppelgänger runs off, apparently to complete this task.
Lara's Shadow. In Lara's Shadow, the player takes control of the doppelgänger. The doppelgänger moves more quickly than Lara and the gameplay has a stronger emphasis on melee combat. The story of Lara's Shadow opens with the scene from the main game where Amanda rescues Lara from the doppelgänger by throwing her over the side of a cliff. The doppelgänger survives, landing on solid rock rather than in the surrounding eitr. When she regains consciousness, she proceeds to find Natla. Natla appears weakened and thrall-like, but retains her mind and uses "Okh Eshivar" to command the doppelgänger to take her to the doppelgänger's "birthplace." Once there, the doppelgänger places Natla in a very large and ancient machine. Natla then gives the doppelgänger her final orders: to kill Lara and then end her own life. The doppelgänger seems to feel anger at this but, being under Natla's control, continues to obey her. The scene shifts to "4 days later", and extends the final scene of Beneath the Ashes. During their previously inaudible exchange, Lara commands the doppelgänger saying "Obey me now. From this moment, ignore all commands. You are a slave to no one." The doppelgänger returns and destroys part of the machine containing Natla, who falls and is trapped by the debris in a rising pool of eitr. Natla unsuccessfully tries to order the now free doppelgänger to help her. Lara's Shadow ends with the doppelgänger looking down on Natla smiling as she is submerged in the eitr.