Tomoya is attending his third year of high school. He is the childhood friend of Kotomi, grandson of Shino, and the only child of Naoyuki and Atsuko. Tomoya has a reputation for being a delinquent, maintaining a very poor attendance rate and is feared by fellow schoolmates. He is rather observant and introspective but he doesn't voice his thoughts.
Tomoya is experiencing a sequential dream which tells a story of an unnamed girl living alone in a desolate world. He sees the dream through the perspective of a doll made from junk that the girl created. Tomoya cannot talk in the dream and he communicates with the girl through gestures.
Through the events of Clannad, Tomoya learns the value of family and his mood improves tremendously.
Tomoya's mother, Atsuko lost her life in an accident when he was very young and he retained no memory of her. Because of the absence of a mother in his life, Tomoya tends to become attached to mother figures such as Nagisa, Sanae, Misae, and Tomoyo. He revealed that his first love was his homeroom teacher during his first year of grade school. Naoyuki had to raise Tomoya alone.
Tomoya was the basketball club captain during his second year of high school. He got into a fight with his father and was slammed against a wall which dislocated his right shoulder. Since then, Tomoya was incapable of lifting his right arm higher than his shoulder. Naoyuki quickly regretted his action and attempted to became friendly with Tomoya. Tomoya saw his father's new disposition as treating him as a stranger and Tomoya developed a strained relationship with his father. Tomoya would try to stay away from his father for as long as possible and returning home late at night after Naoyuki had fallen asleep. This would cause him to wake up late which leads to his poor attendance rate.
Tomoya and his best friend friend Youhei enjoys being late for class, skipping classes, and fooling around at Youhei's dorm room. He has no motivation to concentrate in class but he occasionally wonders about his life and future. Tomoya met Nagisa on the way to school and befriended her. His school days are very busy and he meets many interesting characters. Tomoya would get to know the characters deeper and help solve their problems.
Tomoya's relationship with Nagisa matures further and they spend their lives together. He got a job as an electrician and he worked with Yusuke. Tomoya and Nagisa moved to an apartment and lived together. Eventually, they got married and Nagisa became pregnant. Nagisa passed away giving birth to their daughter Ushio and Tomoya fell into depression. He gave Ushio to the care of Sanae and he drowned himself in work and he picked up smoking.
5 years later, Tomoya discovered his fatherly love for Ushio and took her back to his care. Ushio fell ill and she and Tomoya passed away in the cold of Winter. After obtaining all 13 light orbs, Tomoya was sent back in time and wished for Nagisa's safe delivery. They lived together happily.
Tomoya's dream occurs in the Illusionary World. A new dream sequence introduces a new chapter which describes Nagisa's story.
Tomoya woke up in a run-down hut. He sees a girl caring for him. He learns to walk. Tomoya went outside the hut in a grass field and saw a lot of floating light orbs. He learned that the girl created him and he requested for some friends to be created. The girl created a few animals that ate flowers. Tomoya didn't like the scenery being destroyed but the girl explained that they need to eat to survive.
The girl created a doll as Tomoya's friend. Tomoya tried clapping to make it walk but it didn't come to life. The girl was sad. Tomoya realized that the girl was the last remaining human in the world. He wonders where his consciousness came from. Tomoya requested the girl to create hoppy friends. Tomoya and the girl collected junk to make the friends. She warned Tomoya not to go too far but he did and he got lost. The girl sent the animals to search for Tomoya and to lead him back to her.
The girl created a see-saw and went on to create an entire playground. Tomoya was sad to know that she was the last remaining human. Winter was approaching and the girl started to suffer from the cold weather. Tomoya suggested creating a flying machine to escape the cold. Tomoya collected junk and tried to create the machine. The girl was too cold to create the machine and she decided to walk. At this point, Nagisa explained that the doll knew where the warm world was and was leading them there.
Tomoya and the girl slowly traveled. They were accompanied by the animals that the girl created before. Finally, the girl passed away in the cold. Her consciousness was released and became the consciousness of the Illusionary World. She revealed that she came from the world that Tomoya was from and that Tomoya could freely travel between both worlds. The girl explained that the light orbs were people's happiness. Tomoya was one of the light orbs and she created a body for Tomoya to inhabit. She then sent Tomoya back in time to collect all 13 light orbs to alter his fate. The girl and Tomoya sang the Big Dango Family song and she bade him farewell, calling him dad.
Tomoyo After: It's a Wonderful Life
Tomoya moved to an apartment after he graduated from high school. He works at a garbage management company. His job is to salvage parts from junk and repair electronics. The company only consisted of himself and the boss. Tomoya obtained a driver's license and drives a van to collect junk.
Tomoya enjoys kissing Tomoyo and she was greatly annoyed by it.