Madison Li was born in 2229. She was a young, idealistic scientist when she met James and 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 on a large scale was much harder than first thought. After James and Catherine had a child, things couldn't get any worse for Project Purity when Catherine died and James decided to abandon the project to keep his child safe. The Brotherhood and the other scientists also left, 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.
Nineteen years after abandoning Project Purity, she is older, wiser, and much more cynical. Her life was going smoothly, but things 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, but she refused, thinking too much time had passed. Soon after her talk with James, she meets the now-adult Lone Wanderer. With Dr. Li's directions, the Lone Wanderer locates James, who returns to Rivet City and is finally able to recruit Madison to help him. Along with several other scientists, they head for the Jefferson Memorial, the location of Project Purity.
Once there, the scientists begin repairs to make things operational again. All is going smoothly, but suddenly the Enclave arrives and quickly overruns Project Purity. A squad of troopers led by Augustus Autumn occupies the project control room, demanding that the project be handed over to them at once. James, not trusting the Enclave, refuses to hand over the project. When Autumn, losing his patience, kills Janice Kaplinski, a fellow scientist working on the project, James sabotages the project, resulting in his death. Madison hesitates for a moment, in shock over the death of James and Janice, but then tells the Lone Wanderer that they can escape through the Taft Tunnel. Madison, the Lone Wanderer, and possibly some other scientists, escape and eventually make it to the Citadel. She speaks to Elder Lyons personally and demands that the Brotherhood of Steel take back the purifier.
After the Brotherhood defeats the Enclave at Project Purity, she tells the Lone Wanderer and Sarah Lyons that the equipment has been damaged, whether unintentionally or by sabotage. She further tells the two that the project control room is lethally irradiated, but it still needs to be activated quickly or the facility would explode.
Doctor Li has a unique hairstyle that is unused by any other NPC, as does Cherry.
Unlike Cherry, however, her hairstyle, "The Sophisticate," can be selected for the player character if they are female.
After the escape from Project Purity, Doctor Li no longer has any dialogue 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).