Nobody truly knows what happened to the Lone Wanderer after the events in The Capital Wasteland. That's because they hid it amazingly well.
Emma is a resident in Goodneighbor who, like many others, holds a big secret inside her. She is actually the Lone Wanderer, in search of new adventures after Proyect Purity, only with a different face, skin tone, body shape, voice, and name. One day, the Sole Survivor of Vault 111 stumbles into Goodneighbor at the beginning of her travels, in search of Diamond City. Upon meeting Emma, they embark on an adventure across the Commonwealth together.
Five years after joining the Brotherhood and 4 after joining Trinity, Artemis is sent on her first major mission. To help Elder Lyons in the Capital Wasteland with the Super Mutant threat as well as to take care of a former Brotherhood Paladin named Ashur who turned slaver.
Things become complicated however when she comes across a Lone Wanderer in Megaton who is looking for his father. It's when it's mentioned that his father had a Brotherhood of Steel friend when Artemis takes interest and offers to go with him since she's also on her way to them. On their journey they come across the Enclave, an old enemy of the Brotherhood.
Things come to a head as to who holds the Jefferson Memorial, the sight of Project Purity and war immediately breaks out between the two factions. A war deciding if the region gets fresh, clean water, or to make it so everyone in the wasteland becomes sick.