Fresh from academy and in search of lost relics, a 21-year-old Lara Croft journeys to an island off the coast of Japan aboard the Endurance, a salvage vessel helmed by Captain Conrad Roth. Before anchoring at bay, the ship is cleaved in two by an unforeseen storm leaving Lara separated from any other survivors and washed ashore. She must endure physical and emotional torture in order to survive the island.

The game begins with Lara devoid of any weapons, tools or essentials such as food and water, which the player must search for in order to survive. Sections of the island are restricted to the player until Lara is able to perform specific physical abilities achieved via a "skill system", or obtained the necessary equipment to advance. At frequent base camps throughout the world, the player can combine pick-ups to create new items, improve Lara's abilities and/or fast travel to previously discovered base camps to avoid copious amounts of backtracking. There is a "much larger emphasis" on combat, as instead of using a lock-on aiming system akin to previous Tomb Raiders this game will employ a manual "free aim" mechanic.

The game introduces a "survival instinct" that Lara can use to solve puzzles. It will highlight useful items for use if the player is stuck in solving a puzzle. However, Lara can only do this while standing still. Some elements of the world crumble when Lara stands on them for too long. When the player jumps to grab a ledge, Lara will no longer magnetize to the nearest ledge like in previous instalments. The player will also be able to change direction mid-air. Puzzles will be more complex than previous titles, it will use elements of fire, water, wind, and friction. Helping hands and UI will be kept to a minimum, except for indications of burnable objects, health items, and during quick time events.

On 6 12 2010, Square Enix announced Tomb Raider had been in production for nearly 2 years; "Square Enix Ltd. is excited today to announce Tomb Raider, the new game from Redwood City based studio Crystal Dynamics". Studio head Darrell Gallagher said, "Forget everything you knew about Tomb Raider, this is an origins story that creates Lara Croft and takes her on a character defining journey like no other". Tomb Raider will be the first game in the series expected to receive a Mature 17+ rating in the United States.

Lara Croft's model is animated using compiled performance capture, a technique used in the previous instalment, Tomb Raider: Underworld. The game will be the first to use Crystal Dynamics's game engine called the "Crystal Engine".

On the 3 June 2011, the "Turning Point" CGI teaser trailer premiered at the Electronic Entertainment Expo 2011, emphasising the release date will be the third quarter of 2012.

Keeley Hawes will not be returning as Lara Croft for 2012's Tomb Raider, after completing Tomb Raider: Legend, Anniversary, Underworld and Lara Croft and the Guardian of Light. Her contribution spans an unprecedented four years; the longest role of any of Croft's voice actresses in English. In December 2010, Crystal Dynamics was said to be trialling dozens of voice actresses. a voice actress has been found for Lara Croft, but Square Enix has not revealed her name as of yet.