Alternatives to white guest stars getting treated with kid gloves and Shinwell being fridged for fake ass Joanlock drama:
The beginning of season 2 opens with Sherlock learning of Moriarty’s death in prison. In episode 2x12 they find her daughter and make sure she goes into a loving home after her first adoptive parents are murdered. Mycroft visits for a time but both Joan and Sherlock sense his insincerity from the beginning and Joan calls out his bullshit about saving Sherlock from prison. She also slaps him, both for wanting her to feel sorry for him and expecting his sacrifice for Sherlock to make her forgive him for her kidnapping. Mycroft still fakes his death and leaves their lives forever. Sherlock and Joan have a healthy discussion eventually about why Joan needs to move out. They go solve a case in London together. Joan returns to New York, Sherlock chooses to stay.
Sherlock and Joan exchange letters frequently during the 8 months he’s in London. He tells her about Kitty.
Kitty returns after Gruner commits suicide in prison, leaving no proof or testament behind that it was she who disfigured him. She finds a girlfriend in New York, and they move into a place not too far from the brownstone, and often join Joan and Sherlock on cases. Kitty and her gf have a child through a sperm donor. Kitty is the pregnant one. Joan and Sherlock still become godparents. Joan loves babysitting. Sherlock takes longer to get used to it.
Joan dates Andrew for a while, and discovers she’s aromantic. After discussing this with Andrew, they stop dating but remain good friends and have a sort of open relationship. Sherlock sometimes joins.
When Sherlock relapses and beats Oscar, he accepts a prison sentence for his crimes rather than be blackmailed by his father. Joan and he exchange letters during that time. Andrew and Joan live in the brownstone together for some time, though Andrew goes on frequent business trips. Joan learns more about beekeeping. She, Alfredo, and Kitty visit Sherlock in prison at least once a month each. Joan sometimes visits more often when she’s on a case she knows he’ll like.
After Sherlock gets out of prison, Morland tries to help them on a case. Days later he’s murdered. Moriarty’s successor is behind the crime, and Joan and Sherlock set out to dismantle their empire for good. Sherlock doesn’t so much mourn his father as much as he regrets the man never understood why he always held May’s death against him. Joan and him have a much deeper conversation about May’s addiction after Morland’s death. Joan gets the ring.
Sherlock and Fiona date for a few months but decide they’d rather be friends. Sherlock loves sharing his work with her, but understands he can’t share everything he wants because there are some things she’s not comfortable with. She helps him begin to like cats again. Fiona frequently visits the brownstone, and Joan always makes her favorite tea, and they talk about the bees, poetry, technology and computers, different developments in their respective fields.
Shinwell survives. Joan avenges him and makes the first inroads in dismantling SBK while Shinwell is hospitalized. Sherlock comes to understand Shinwell wanted to make amends for his friend’s murder just as much as he wanted vengeance. He tells Sherlock he would’ve never let any harm come to Joan - he would’ve rather died. Shinwell confesses to the murder and goes back to prison. Joan and him exchange letters for the rest of their lives. The three of them collaborate on cases, rather covertly sometimes, as Shinwell forms different alliances in the prison system.