The Silver Samurai is the greatest villain of Japan. From behind the scenes, he basically runs the entire country. He has a large army of ninja at his disposal. Despite being a villain, he does follow the samurai code of honor. He is also a longtime enemy of Tony Stark, whom he considers a rival and worthy opponent.
It’s unknown how he and Stark ever became enemies. At some point in the past however, Stark rescued Silver Samurai’s sister from an attack by a rival crime organization. This allowed Silver Samurai to overthrow his rival and become the greatest crime lord of Japan.
After the Avengers are forced to leave America due to the new Superhuman registration act, Tony and Akira visit Silver Samurai to ask for his help. In return for saving his sister once, Tony Stark asks Silver Samurai for a temporal cease-fire and his promise not to ally himself with Loki. Silver Samurai agrees to these terms, on condition that Akira, whom he doesn’t hold in high regard, agrees to a duel. The duel consists of a test to see if Akira can D-smash Iron Man faster than Silver Samurai can draw his katana and slice the boy in half. Akira reluctantly agrees, and actually passes the test, earning him the respect of the samurai.
In the final battle with Loki, Silver Samurai actually came to Iron Man’s rescue when the hero was about to be killed by the Asgardian god, since he didn’t want any other villain to have the honor of killing Iron Man. In this fight, he teamed up with Iron Man’s other archenemy, Mandarin, to fight Loki. They were able to keep Loki at bay long enough for Akira to bring the Kree Mact to Iron Man, which gave him the power he needed to defeat Loki. It's unknown what became of Silver Samurai afterwards.