As King Arthur was in fact Arturia Pendragon, it should have been impossible for her to father a child. However, Arturia's sister Morgan enchanted her with sorcery; due to Merlin's subsequent magecraft, Arturia was temporarily transformed into a pseudo-male. Mordred is a homunculus created from sperm extracted from Arturia during that period. He developed within Morgan's ovary and was born as a complete male clone of Arturia. As a homunculus, Mordred had a much higher growth rate and a shorter lifespan than a human.
Morgan raised him as her son, telling him that if he hid his status by never removing his helmet and obeyed the king, he would some day defeat the king and inherit the throne. Despite being a masked knight of unknown origins, his abilities in swordsmanship and straightforward chivalry earned him a place in Camelot; he became one of the Knights of the Round Table on Morgan's recommendation. He bore the obsession placed on him by his mother, but at the same time, his childish innocence caused him to adore Arturia and worship her as the "perfect king."

Ashamed over his twisted birth, Mordred held an unconscious envy towards normal people. He suppressed that emotion in order to strive hard to be an ideal knight that protected the way of the knights in such a way that could only be found in picture books. Morgan eventually shattered his innocence by revealing that he was a child born between her and Arturia, and that the king would never accept such a filthy child. Initially, he was proud to be the son of the king, even thinking it a blessing to be a superior homunculus, capable of succeeding the king in name, mind, and body. Unfortunately, Arturia completely rejected him, and refused to recognize him as an heir. Mordred believed the reason that he was not accepted was due to the hatred Arturia bore Morgan, and that no matter how much he worked to excel over others, he would forever be viewed as a tainted existence. The love he had for the king up until that point was so great that Arturia's rejection made his hatred burn.

Mordred exploited the growing distrust of the Round Table towards Arturia and rebelled while she was on an expedition to Rome. Camelot fell under his control. He became the leader of the rebellion, representing the national discontent towards their king and claiming that he was the one fit for the throne. Though Mordred claimed to hate the king, his true wish was for Arturia to call him "son."

During their final clash on a hill of swords, he lamented that the country was destroyed beyond repair, and that he would have prevented it had he been given the crown. He asked Arturia, "Did you hate me, the son of Morgan, that much?!"; Arturia emotionlessly replied, "Not once did I despise you. There was only one reason I would not give you the throne. You didn't have the capacity of a King."
Defeated in single combat, Mordred's final blow struck true against Arturia. Impaled by her spear, the helmet forced upon him shattered, revealing the face identical to Arturia's. With his blood-soaked hands, he reached out to touch the king at least once while saying "....Fa-ther." His final wish went unfulfilled as he fell.