The season finalé devolves into a complicated game of villainy politics. The short answer seems to be that Vikner wanted Morland Holmes dead because others in the organization were lobbying to tap Morland as their new leader in Moriarty's absence. Vikner had the attempt made on Morland's life, which sidelined him as he was too wrapped up in Sabine's death. But now it seems Morland might again be able (and willing?) to step in.
Which he does. After swimming through a bunch of relative nonsense, the upshot becomes Morland having Vikner killed and accepting the role of head of Moriarty's Web of Intrigue (TM). One can't help but wonder what Moriarty would think, given she knows how much Sherlock dislikes his father. Also, if Vikner was the father of Moriarty's daughter and is now dead . . . Where is this child? Who is caring for her? (In truth, we have no reason to believe Vikner was taking care of her either. In fact, Moriarty hadn't wanted him involved if I remember correctly? But it's still a worthy question.)
Sherlock is naturally put off by the idea of his father as evil mastermind, though isn't that how he always thought of him? So maybe it's the association with Moriarty in particular that turns his stomach. But Morland tells him the plan is to destroy the organization from the inside out. Do we believe that? Does it really matter?
Morland also says they will no longer operate in New York, but that seems ridiculous. New York must be very fertile ground for that kind of work. Saying your son is off limits is one thing, saying an entire major city is? I'd question that leadership.
In the end, Morland leaves Sherlock his safe house, and Sherlock in turn tries to give it to Watson. Morland pricked Sherlock's conscience by suggesting Watson was not safe in his company, that she was made vulnerable by association with him, so he was seeking to distance her. She didn't go for it. But in an astounding show of lack of forethought, she also suggested setting Marcus up with her sister.
The episode felt very tidy, and so I have to think they weren't sure whether they'd be getting another season at the time they wrote and filmed it. I'm actually still a little surprised they did given the move to Sunday and the slump in viewership. This would have been a fine place to end it, but there's room for more story too. See you (and them) again in the fall.