Into one place
The chaos of the worldwide waters was incompatible with the controlled environment needed for life to begin. The action on the third day would bring order to the turbulence.
The preposition אֶל ('el, "ale") moves the subject towards a destination, sometimes even within it. What used to cover the surface is said to have moved to a specific place, the מָקֹ֣ום (maqom), literally a place of standing.