We don't see Tobias's mommy dearest, Evelyn, too much in Allegiant, but her actions are hugely influential on the course of events, and on Tobias himself.
The events of Insurgent leave Evelyn in power, and it ain't pretty. Evelyn runs Chicago as if were 1984 or The Giver, enforcing curfews and totalitarian-style work schedules and exiling anyone who gets in her way. She's basically traded one dystopia for another. It's good for her, now that she's in charge, but things aren't looking so rosy for anyone else.
The fact that Evelyn gives up her power in the end in exchange for a relationship with her son might come as a surprise. But looking at it more closely, it makes total sense. When Edward dies early in the novel, Evelyn takes it pretty badly. Tobias notices: "I never knew they [Edward and Evelyn] were so close, but I can see it now, in the gleam of tears in her eyes and the trembling of her fingers. It's the most emotion I've seen her show since I was a child" (6.45).
This hurts Tobias, who feels that Evelyn couldn't care less if Tobias, her own son, died. But Edward's death is a reality check for Evelyn. It's her policies—and the social unrest they've caused—that resulted in Edward's death. If his death was that hard for her, how difficult would the death of her own son be, especially if it, too, would be all her fault?
Whatever the reason, she chooses Tobias over power in the end, and she doesn't seem to regret it a bit.