The story of the 100 acre plot begins with the Phelps - Gorham Purchase but the story of Western NY goes back further. Rather than recount the detailed story here the following links give the necessary information.
For our purposes suffice it to say that a dispute between New York and Massachusetts over Western NY was settled at a convention in Hartford, Connecticut in 1786. New York would govern the area but Massachusetts would have the preemption rights; the rights to buy the land if the Indians decided to sell it. Land speculation was rampant at that time and several groups were negotiating with the Iroquois to buy the land. Understanding the situation Phelps and Gorham purchased the Preemption Rights from Massachusetts and completed a purchase of land from the Indians in July 1788.
The sale included a 20,000 acre Mill Lot on the west side of the Genesee River. The following is taken from Indian Allan's Mills by Blake McKelvey, Rochester History, Vol.1, No. 4, October, 1939.
"The Mill Lot sold to Phelps and Gorham by the Indians at Buffalo Creek in July, 1788, was planned by the Indians as a means to help them bridge the chasm that separated the Indian from the white man's culture. The mills to be erected at the falls were to grind the grain produced by the Indians; with this stimulus at hand, the leaders of the tribesmen hoped to adjust their people to an agricultural way of life, and thus to enable them to live in peace and harmony with the white settlers soon to locate east of the Genesee. The original purpose of the Mill Lot was for many causes never realized, and Allan's mills became, instead of a link between the cultures of white and red men, a useful outpost for a few years, of the western-moving New York - New England frontier."
"On 30 Sep. 1788: N. Gorham and O. Phelps & Co., by their agents Wm Walker, Caleb Barton and Benj. Barton articles to Ebenezer Allan the privilege of a grist mill and saw mill with lands sufficient for mill yards and roads to the same and like-wise 100 acres of land adjoining the same; ...and to build a good grist mill and saw mill by the 1st of June next."
Allan built the saw mill first and used it to cut the wood for the grist mill.
"The small stream which Allan plowed open for a raceway possibly branched off from the river near the present western end of the Court Street Bridge and ran north to tumble down an extension of the rock ledge that formed the cascades, .... After dropping over this ledge, the stream or raceway ran northeast across the marshy lowland until it rejoined the river somewhere near the location of the western end of the present Main Street Bridge. A small island was thus formed … Allan's mill stood on the mainland west of the raceway, and a low platform bridged the race and connected with a shanty built on the island as a cook house."
The following map from the McKelvey publication shows the layout.
The above map also appears in the Rochester Historical Society Publication Series in Centennial History of Rochester, N.Y., Vol. 1 Beginnings, 1931. It is bound between pages 154 and 155. The map was made by Major Wheeler C. Case, in collaboration with Morley B. Turpin.
The following is from an 1934 map republished in 1984 for Rochester's Sesquicentennial.
Using present day streets, the mills were west of the Genesee River, east of Exchange Street, south of Main Street and north of Broad Street (the old Erie Canal).
Allan's 100 acres was "to be located in as near a square form as the winding of the river would permit, commencing at the center of the mill and extending an equal distance up and down the river, then back so far as to contain 100 acres in the above form."
The approximate location to the original 100 acre plot today would be the Genesee River on the East, west to the intersection of Broad and W. Main, the Inner Loop on the north and Troup Street on the south.
Allen sold the mill site to Benjamin Barton in March 1792. Charles Williamson acquired the property in 1794 for Sir William Pulteney. The mills fell into a state of disrepair and were likely abandoned by 1804. The 100 acre plot was purchased by Nathaniel Rochester, William Fitzhugh and Charles Carroll on November 8th, 1803. The mill seat was neglected until after the War of 1812 when development began. It should be noted that Nathaniel Rochester did not move to the village bearing his name until 1818.