A post-"The Abominable Bride" AU where Sherlock didn't overdose and figured out someone was behind the Moriarty video and he wasn't the real threat after he got of the plane. He goes to Bart's to make sure Molly is safe, then convinces her to go to Baker Street first for the night after he was supposed to leave and eventually longer as he tries to figure out who was behind the video. Series 4 goes differently; Mary survives the attempt at the aquarium after John saves her life, but Mycroft, John and Mary decide it's best if Mary fakes her death and stays somewhere safe while Mycroft works of neutralizing the rest of her enemies. As John is aware of her death and Sherlock and Molly aren't, the dynamics of "The Lying Detective" are different (Sherlock doesn't go on a drug binge and John doesn't take his anger out on Sherlock) and the truth comes out in a modified version of "The Final Problem" where Eurus reveals the truth to Sherlock, who understands but is still a bit hurt his brother and his best friends didn't trust him with the truth.
Molly was living at Baker Street at the time of the bombing, though she wasn't at Baker Street when it happened (she was at work at Bart's) so she's distraught when the phone call happens and is so relieved that Sherlock and John are alive and to hear Sherlock's voice for herself, and he confesses he loves her without her forcing him to, getting a love confession in return. After Eurus goes catatonic Sherlock goes to Molly and tells her everything, and they stay at her flat while Baker Street is being rebuilt, and she gets introduced to Eurus after the visit that Eurus had with Mycroft, Sherlock, Siger and Violet, and she speaks again. The rest of the series is Sherlock navigating his relationship with his family as well as Molly, Mary's eventual return, and his eventual return to Baker Street with Molly by his side. Primary ship focus is Sherlock/Molly, but there's stuff with John/Mary and Mycroft/Lady Smallwood as well.
