Tomoyo´s story starts of with "dumping" Nagisa from the start. *gg*
After her performance with the bikers, Sunohara thinks she might be a guy and uses his plans to prove it (of course, with painful results).
Still, Tomoyo starts to get interested in Tomoya and comes to wake him later on. Soon after, they get in the classical girl-/boyfriend relationship. Still, since he is a delinquent and she aims for beeing the student council president, they decided to break up if she should win the election.
She quite often came to wake him up and cook for him, and he started to help her to lose her "dangerous girl"-image, like having a match against the other clubs to increase her popularity. Later on, she tells him about her little brother and that she wants to be the student council president to save the cherry blossom trees at the hill in front of the school.
And then it finally happens, while meeting with Tomoya in his empty classroom and the massage of Tomoyo´s election arrives per speaker, instead of breaking up, they have their first kiss.
But soon after that their problems start, since no one approves of Tomoyo and Tomoya beeing together and they start to pressure him that he should break up with her since she may be able to face a bright future if she isn´t with him.
After quite a long time of thinking, he made the painful choice to break up with her so she can fulfill her dreams. After a while, Tomoyo accepts it...
After graduation (several months later), he meets her on a snowy day on that hill and she tells him that she was able to reach her goal, but that it saddens her that she had lost so much time to be with the one she loves... *huge hug*
Some time after that, Tomoya started to work and meets up with Tomoyo and her brother that are going to school and leaves shortly afterwards; and she forgot to give him his bento *gg*