It is said that during the Satya Yuga, people on Earth became irreligious and disorderly in their behaviour. This is when the Gods decided to flood the earth in order to prepare it for the renovation process. Lord Vishnu had given Lord Brahma, the creator, the instructions to rebuild the earth. These guidelines were the Vedas, Hinduism's four primary books. Lord Brahma decided to take a break before embarking on this monumental task because he was exhausted from the process of creation.

At this time, a horse-headed demon named Hayagriva (not to be confused with Lord Hayagriva, Vishnu's avatar and a symbol of wisdom and knowledge) emerged from Brahma's nose and stole the Vedas. Then Hayagriva went and hid himself deep within the earth's oceans. Meanwhile, a pious king named Satyavrata, a great admirer of Lord Vishnu, worshipped Him on a regular basis and wished to meet Him. So Lord Vishnu decided to pay Manu a visit.

The story, according to the Matsya Purana, goes like this :

Satyavrata, the king of pre-ancient Dravida and a Vishnu devotee who later became known as Manu, was washing his hands in a river when a small fish swam into his hands and begged him to save its life. He placed it in a jar, which it quickly outgrew. He then transferred it to a tank, a river, and finally the ocean, all to no avail. The fish then revealed himself to be Vishnu and warned him that a deluge would destroy all life in seven days. Manu was told by the fish that at the end of the Kali Yug, the mare who lived at the bottom of the ocean would open her mouth and release a poisonous fire. This fire will consume the entire universe, including Gods, constellations, and everything else. The seven clouds of doom would then flood the earth, transforming it into a single ocean.

As a result, the fish instructed Satyavrata to construct an ark that would carry "all medicinal herbs, all varieties of seeds, and accompanied by the seven saints," as well as the serpent Vasuki and other animals. As the flood approached, Manu's ark was finished. As the flood swept over the land, Manu asked Vishnu why mankind had to suffer such a calamitous fate, to which Matsya Vishnu replied that he was the only moral man alive and would be the father of future generations of men. Matsya killed Hayagriva and gave the Vedas back to Brahma. Then, using Vasuki as a rope, he tied himself to Manu's ark and protected them from the storm and floods. When the storms passed and the water receded, Matsya Vishnu left Manu and the others in the Himalayas to restart human civilization.