The Madison Junction-to-Toronto route was part of a secondary Santa Fe line that originally extended as far south as Benedict Junction, a connection with another Santa Fe line that ran roughly east-west through Chanute. Toronto was midway between Madison Junction and Benedict Junction, and a Missouri Pacific line crossed there. The Missouri Pacific line lasted beyond the 1982 Union Pacific acquisition but has since been abandoned.
The ATSF route between Virgil and Benedict Junction (including the Virgil to Toronto segment) was abandoned some time between 1936 and 1950. The northernmost segment, from Madison Junction to Virgil, was abandoned some time between 1950 and 1964.
This ATSF route roughly paralleled the Verdigris River. South of Toronto, Toronto Lake was created across the river; the Cross-Timbers State Park covers the surrounding area, and appears to include the right-of-way. The lake was formed by a dam built between 1954 and 1960.
Thanks to Mike Palmer for contributing information about this route.