The OVA tells the story of how protagonist Himura Kenshin becomes the Hitokiri Battōsai and how he obtains his infamous cross-shaped scar. Himura is six years old at the outset of the OVA and eighteen by its conclusion. The OVA is set during the final years of the Bakumatsu up through the start of the Boshin War.
In 2003, Trust and Betrayal was collected into a two hour feature-length motion picture with new animated sequences and released in North America as a Director's Cut DVD.
During his time as a Hitokiri, Kenshin kills a bodyguard named Kiyosato Akira, who is the fiancé of Tomoe. The encounter with Kiyosato leaves Kenshin with the first half of his cross shaped scar.
After a fight with an assassin, Kenshin meets Tomoe. Kenshin takes her to the inn where he is residing, where the owner mistakes her for a prostitute and nearly sends her away. The presence of her there brings a sort of relief to the stressed men of the Choshu clan, but raises the suspicion of the leader, Kogoro Katsura, who has her investigated covertly.
After the Ikedaya affair, when Kenshin's cover as the shadow Hitokiri is blown, Katsura arranges for Kenshin and Tomoe to hide in the village of Otsu. After a few months, Tomoe's brother Enishi comes to visit and secretly reveals to his sister that the shogunate spies assigned to track down and kill Kenshin are close by, and that her revenge will be complete. After sending off Enishi, Tomoe leaves the house and tries to persuade the shogunate men to give up their pursuit of Kenshin, and attempts to kill their leader.
The morning of his wife's disappearance, Kenshin is visited by a comrade who tells him that the one who set the assassin on him was Tomoe and that she is meeting at that moment with her co-conspirators.
On his way toward the house where Tomoe is supposed to be, Kenshin faces three of the four shogunate agents and is badly injured. While Kenshin is fighting with the fourth agent, Tomoe steps in between the two persons and gets killed by accident. Before her death, she gives him the second part of his cross-shaped wound. Kenshin takes her death hard and swears after burning her body to fight to bring about the age desired by his employer Katsura, and after that to continue fighting to protect down-trodden people without taking another life.