Madison Li was born in 2229. She was a young, idealistic scientist when she met James and was fully bought into the notion of Project Purity. Madison hid her growing romantic feelings for James while respecting his marriage to Catherine. The project was going smoothly and even had the support and help of the Brotherhood of Steel, but soon it all went downhill. Super mutant attacks were more frequent and purifying water was much harder than first thought, and after James and Catherine had a child, things couldn't get any worse for the project as Catherine died. James decided to abandon Project Purity to keep his child safe. The Brotherhood and scientist also abandoned the project and Project Purity was put on hold.
Dr. Li is the first distinct face that the player sees, during the birthing scene, as she carries the newborn Lone Wanderer away while Catherine is going into cardiac arrest.
Although Madison Li was filled with remorse upon Catherine's death, her sadness was replaced with a powerful sense of betrayal after James abandoned Project Purity. She headed to Rivet City, hearing about its thriving scientific community set up by Horace Pinkerton. Soon after she arrived, she began to argue with Pinkerton as they often had different views on the matters at hand. One day having enough of it all, Pinkerton left Rivet City and began to live in the bow of the ship. Doctor Li soon became head scientist of the group and began to grow healthy, radiation free produce like fresh apples and fresh pears.
19 years after abandoning Project Purity, she is older, wiser, and much more cynical. Her life was going smoothly but was drastically changed when she got an unexpected visit from James, who had escaped from Vault 101 and returned to Rivet City. He tried to recruit Dr. Li in his efforts to revive Project Purity. She refused, thinking too much time had passed. Soon after her talk with James she meets the now adult Lone Wanderer and tells them the location of their father. James and the Lone Wanderer return some time later and James is finally able to recruit Madison to help him and with some other scientists they head for Project Purity.
There, the scientists begin to make things operational again. All is going smoothly, but then the Enclave arrive out of nowhere and they quickly overrun Project Purity. A squad of troopers, led by Augustus Autumn quickly occupy the project control room, they demand that the project be handed over to them at once. James, not trusting the Enclave, refuses to hand over the project, Autumn starts to lose his patience and kills Janice Kaplinski, a fellow scientist working on the project. James then sabotages the project, resulting in his death. Madison hesitates for a moment, and is in shock over the death of James and Janice, she then tells the Lone Wanderer that they can escape through the Taft Tunnel, Madison, the Lone Wanderer and possibly some other scientists escape and after running into several Enclave troops and feral ghouls they eventually make it to the Citadel where she then rests.
During Take it Back! she tells the Lone Wanderer and Sarah Lyons that the project needs to be activated now or the facility would explode.
After the purifier is activated, Madison leaves the Capital Wasteland and travels to the Commonwealth to pursue other scientific purposes, allegedly because she could not stand the BrotherhoodScribes' involvement in Project Purity. However, it should be noted that it is mentioned in the game that she could be slightly tolerant to Scribe Rothchild.
Doctor Li has a unique hairstyle that is unused by any other NPC and unavailable to the player, similarly to Cherry.
After the escape from Project Purity, Doctor Li no longer has any dialog available with the Lone Wanderer, she just wants the player to leave her alone.
The door to her quarters is always locked and must be picked to gain entry.
Unlike most beds in the personal quarters of Rivet City residents, Dr. Li's bed is classified as unowned. This sometimes results in NPCs appearing at her door fruitlessly attempting to gain access to the open bed, or spawning in her room during their assigned sleeping hours (trapping them inside).