Madison Li Doctor Madison Li is a scientist working on portable fusion power and hydroponics experiments in Rivet City in 2277 . As of 2287 , she is in the Commonwealth working for the Institute as the head of their Advanced Systems division . Background . Early Life and Project Purity . 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 character sees , during the birthing scene , as she carries the newborn Lone Wanderer away while Catherine is going into cardiac arrest . Rivet City . Although Madison Li was filled with sadness upon Catherine ' s death , her grief 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 pears . It was here in Rivet City that Madison first heard tales of the Institute , a legendary organization that was formed from the ashes of the Commonwealth Institute of Technology from a man named Zimmer ; the Institutes ' s director of the Synth Retention Bureau . Return to Project Purity . Nineteen years after abandoning Project Purity , Madison 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 . Madison once again finds herself working on Project Purity and begins to help her fellow scientists repair the facility to operational level once more . 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 some other personnel , 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 . Long Road Ahead . After the purifier was activated , Madison left the Capital Wasteland and traveled to the Commonwealth to pursue other scientific endeavors . The Brotherhood stayed in the Capital Wasteland with a large military presence , something Li disagreed with , believing that with Project Purity activated and the Enclave destroyed , the Brotherhood no longer needed to remain . However , the real reason Madison fled to the Commonwealth was because she feared for her very life . While Lyons had allowed her to leave unscathed , there were others who believed her to be a security risk . Knowing this information , she fled to find the Institute , the only safe haven she could think of . Mankind Redefined . After a long journey , Madison eventually found herself in the Commonwealth and quickly managed to find the scientific haven that Zimmer spoke about back in the Capital Wasteland . By joining the Institute , Madison embarked on scientific endeavors she had only dreamed of and even managed to become the director of the organization ' s Advanced Systems division . Yet something irks Madison - most notably the lack of transparency ; not getting the full story on everything that occurs within the Institute due to the organization ' s constant burying of facts it finds inconvenient . Li was friends with Brian Virgil . When , several months earlier , he escaped from the Institute , he was declared dead and his lab sealed off against Madison ' s insistence on a thorough investigation . However , the key problem is that she feels the Institute is selfish . The technology that could improve countless lives is hidden inside the Institute , buried deep beneath the ground , yet the Institute continues to hide and isolate itself from everyone . Interactions with the player character . " Fallout 3 " . Effects of player ' s actions . If the Lone Wanderer has killed Three Dog before completing the Galaxy News Radio quest , the player will need to talk to Dr . Li to resume the plot . Other interactions . If the Lone Wanderer passes a Speech check before going to Project Purity , Dr . Li rewards them with 5 stimpaks . Appearances . Madison Li appears in " Fallout 3 " , " Fallout Shelter " and in " Fallout 4 " . Li is also mentioned in the " Fallout 3 " add - on " Broken Steel " . Bugs . Similarly to above , if the player convinces Li to join the Brotherhood but then destroys both the Institute and the Brotherhood along with the Prydwen and the airport , Li can be found standing in the Prydwen ' s burnt - out carcass , wearing her BoS attire and acting like she never left the Institute and the Sole Survivor was made its director .