This manual was first mentioned indirectly towards the end of ''Return of the Condor Heroes'', and formally appeared in the sequel ''The Heavenly Sword and the Dragon Saber''. In the story, the manual was found by the protagonist Zhang Wuji, where it was stuffed into the stomach of a giant gorilla.
Jiu Yang Zhen Jing's history is sketchy. It has been rumored that Shaolin's founder, Bodhidharma or Da Mo, was the creator of the Jiu Yang Zhen Jing, but this has never been verified. The Jiu Yang theory was never written on a single book of its own. Rather, it was written between the lines of Lanvakatara Sutra, one of the many Buddhist Scriptures available in Shaolin. Therefore, its existence was unknown to the pugilistic world until the end of the The Return of the Condor Heroes storyline, when the Mongolian thugs Yin Kexi and Xiao Xiangzi stole the manual from Shaolin Temple. Despite the common belief about the buddhist origin of manual, Zhang Sanfeng doubted this as he delves further into the text. He noted that the philosophy inside is quite Taoist in nature. Zhang Sanfeng also pointed out that the text was written in Chinese characters rather than Sanskrit, the language Bodhidharma would had used. These principles also give Zhang Sanfeng inspirations, which lead to the creation of his Tai Chi Quan.
Shaolin librarian Jue Yuan and his young disciple, pursued Yin Kexi and Xiao Xiangzi to Hua Shan, where the newly-named New Five Greats were paying their respects to fallen Northern Beggar Hong Qigong and Western Venom Ouyang Feng.
With the help of Yang Guo, Zhang Junbao was able to thwart Yin Kexi and Xiao Xiangzi, but the Jiu Yang Zhen Jing was nowhere to be found. Unbeknownst to all present at Mount Hua, Yin Kexi had hidden the Jiu Yang Zhen Jing in the abdomen of a large ape. Later on, Yin Kexi and Xiao Xiangzi fought each other over the manual, a bloody duel that resulted in Xiao Xiangzi killed and Yin Kexi fatally wounded. On his dying words, Yin Kexi made a confession to Kunlun Sect elder He Zudao, asking him to tell the Shaolin people where the manual was kept. Yin Kexi, however, slurred the final statement, and instead of hearing "The book is in the monkey", He Zudao heard "The book is in the oil", which mystified everyone for a century.
Jue Yuan, as the Shaolin librarian, had already read the entire text of the Jiu Yang Zhen Jing and practising based on its principles , giving him extremely powerful inner strength. He also taught a small proportion of these principles to his apprentice, Zhang Junbao, giving him a powerful basic for kung fu learning. Three years later, there as was a challenger at Shaolin. None of the monks were able to defeat him, except Jue Yuan. However, because Jue Yuan was not authorized to learned martial arts, he had violated one of the rules in Shaolin, that is punishable by death. Thus, he and Junbao were to be put to death. Though he is willing to accept that sentence, he begged for Junbao's life but was denied. In desparation, Jue Yuan broke loose, and ran away with Junbao. , the youngest daughter of Guo Jing and Huang Rong, happened to be a the foot of Shaolin and tried to defend Jue Yuan. They were however, no match for the full force of Shaolin temple as well as the fact that they didn't want to harm any of the attacking monks. Jue Yuan carried both away to safety but he overexerted himself. Before his death, he managed a deathbed recital of the text that was listened by Zhang Junbao, , and a high-ranking Shaolin monk named Wu Se. Each of them were able to memorize various parts of it. Because the natures and levels of their kungfu are different, their understandings of the text varied. Zhang Junbao and were able to incorporate various principles of the Jiu Yang Zhen Jing into their personal kungfu and the kungfu of the sects they eventually founded, Wudang Sect and E'Mei Sect, as did Wu Se for Shaolin.
No one, however, possessed the complete Jiu Yang Zhen Jing again for a century until the young hero Zhang Wuji, the injury-tortured son of Zhang Sanfeng's fifth student Zhang Chuisan, found the ape that Yin Kexi had hidden the Jiu Yang Zhen Jing in a century earlier . Kind-hearted and well-taught in medicine, Zhang Wuji liberated the books from concealment in the ape's abdomen. The 15-year old Zhang Wuji spent the next five years learning the Jiu Yang Zhen Jing; soon after the completion of his studies at age 20, he stumbled upon the sacred Ming Cult kungfu Qian Kun Da Nuo Yi , making him one of the most powerful martial artists of his time.