While on a mission Rin and Kakashi were attacked, during that moment Rin was secretly kidnapped by Madara Uchiha under the guise of Kirigakure 's doing and was forcibly made into the jinchūriki of the Three Tails Isobu.
MAJOR SPOILER ALERT AHEAD! Basically, Madara Uchicha manipulated the Mist Village into forming Rin Nohara into the three tails Jinchuriki in such a way that in the chaos, Rin would be killed by the hand of Kakashi Hatake in the presence of Obito Uchiha, for two greater purposes.
Missions can also be classified as S-rank, these are the highest paying and most dangerous type of mission a ninja can go on. These missions are exclusively assigned to highly skilled jōnin or large squads of ninja. S-rank missions pay at least 1,000,000 ryō.
Well, the S-Rank is only used for missing-nin in canon, so Naruto never became one. And the only examples of S-Rank shinobi we have are the Akatsuki member, including Orochimaru.