You will find the Haligtree Roots Site of Grace here, from here, make your way down the stairs to access her arena. As mentioned, there are two phases to the Malenia boss encounter in Elden RIng.

To get the Remembrance of the Rot Goddess you must defeat Malenia, Blade of Miquella, the final boss of the Miquella's Haligtree legacy dungeon. Malenia is found at the very base of the Haligtree ...