At the time of the deluge, there was only ‘Sat.’ In other words, there was only Lord Narayana. There was only One thing. What this means is that there wasn’t another like that One. All of what now exists was there, but not in the forms in which they exist now. The One manifested as many and in different forms, said V.S. Karunakarachariar in a discourse.
There is a story in the Brihadaranyaka Upanishad, which helps us understand this. King Janaka performed a yaga and was going to gift a thousand cows to the foremost among the sages assembled there. When the King said the best among the sages could take the wealth, Yaajnavaalkya ordered his student to take the cows.
Yaajnavaalkya was subjected to intense questioning by the other sages. Uddalaka asked Yaajnavaalkya if he knew of the One who resided in all. Yaajnavaalkya answered that the One who resided in all was the One who resided in the Earth, had the Earth for His body, and yet differed from it. It was He who directed the Earth and remained beyond the understanding of the world. He was the One who was the antaryamin of Uddalaka and of Yaajnavaalkya and of everyone else. Yaajnavaalkya went on to say that He was the One who lived in water, had water for His body, directed water, differed from it and so on. He made similar statements regarding the One being in the Sun, Moon, stars, and jivatmas.
Now, Yaajnavaalkya said the Earth was His body. But we understand a body as having limbs, eyes and ears. So how can the Earth be a body? A snake has no limbs. Does that make it devoid of a body? A doll has legs, hands, eyes and ears. But does it have a living body? So clearly the definition of a body is different from the way we define it in common parlance. Ramanujacharya said a body is that which is supported and directed by an intelligent being, and is inseparable from Him. By this definition, the Earth is supported and directed by God, and since He resides in all, the Earth may be taken to be His body. Likewise, the argument may be extended to water, fire, sun, moon and jivatma. Thus, everything emanates from Him and has its existence because of Him.