The characters Mina, Royal, and Elro join Robin's party at certain times throughout the game; they may assist in boss fights or become controllable by the player.

By finding materials in treasure chests, Robin can craft Tweaks, which provide small gameplay bonuses such as increased melee damage, faster running speed, or unique abilities.

She lives in a world where the sinister religious authority the One Concern, ruled by a being known as "Mother",[3] has taken over the government, and allows only licensed mechanics to handle the power source called "Ivory" that drives its machines.

Those who survive but become mutilated in the process become Agents, legal enforcers possessing extraordinary strength, long lifespans, and a range of superpowers; those who flawlessly survive the process, such as Mother and her successor Royal, are extolled as Mediums, destined leaders of the human race, possessing telekinetic power over all matter containing Ivory.

A conflicting religion is practiced by the Isi, a people who live underwater thanks to excavated technology, powered by harvesting Ivory from the ocean floor through different means than those of the surface dwellers.

As punishment, the house is destroyed, killing his family, and Robin is thrown in prison where she befriends and escapes with Mina, a member of an outcast religious group called the Isi.

Royal helps Robin evade General Chrome, chief of the Concern military, and Mina takes them both to the hidden settlement Isilugar.

They fend off a Concern attack, killing agent White in the process, and Black retreats after taking Mina's partner Samba captive.

The search for Samba brings Robin, Elro, and Mina to a secret Concern structure where children are being brainwashed to form the foundation of a new, cult-like society.

As the One Concern collapses into civil war, Chrome corners the group and prepares to execute them to clear the field for his new regime, but is himself killed by Elro.

Robin, optionally accompanied by Mina depending on dialog choices, goes to its landing site and exploits the damage Royal did to incapacitate it.

In the end credits scene we see what happens to some of the other people of the planet: doctor Gustavo and Teegan start studying their new surroundings post-crisis situation, the ChemiCo Contra rediscover a way to use electricity, Tolo mourns General Chrome's death as the rest of the soldiers recognize him as his new leader, Mina and Samba reunite and share a kiss, Mendeleev furiously cries as Nobel accompanies her and Ash looks at them in the distance before disappearing just as Nobel turns around, Emmet Darland lies in the peak of a snowy mountain alone and lost, his position of power and place in the world now gone, people of the Bastion suffer the consecuences of Chrome's insurrection, the isolated members of the tower struggle to find a new purpose in life and Samba and Mina look forward into the new future their friend has given to them.