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Tris and Tobias constantly find themselves at odds with each other. At one point in the story, when Tobias refuses to listen when Tris tells him she doesn't think they should help in Nita's plot to undermine the power of the Bureau, Tris ends up angry at Tobias when she was right. Nita had been lying to them -- saying they were going to steal memory serum, when they were really trying to steal death serum -- and the plan resulted in Uriah's deathly coma. Tris and Tobias don't talk for days, but it is eventually her capacity to love and forgive him that mends their relationship. If not for forgiveness, slight wrongs and misdoings would ruin the friendships that the group from the city has. In such an unknown place as the Bureau, they cannot hope to survive without forgiving each other and sticking together.
Later in the story, forgiveness comes back into play when Caleb is preparing himself to sacrifice his own live to reset the Bureau officials in the Weapons Lab. Tris knows that he is only doing this to get away from his own guilt; he can't live with himself. She tells him that she forgives him, and she forces him to let her take his place in the Weapons Lab. If she hadn't done this, Caleb probably would not have succeeded in setting off the memory serum. More importantly, Tris wouldn't have been able to live with herself had she let Caleb die.
One last example of this theme occurs between Tobias and his mother, Evelyn. Tobias enters the city prepared to reset the memories of one of his parents in order to stop the city from entering a civil war. Instead of resetting his mother, he tells her that he will forgive her, that he'll be her son again, if she stops trying to rule the city. She agrees, wanting nothing more than reconciliation with and forgiveness from her son.