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The station was in service for six months in 1966 as part of an experiment where all Toronto subway lines were interlined. The experiment was a failure, as any small problem could hold up much of the system. Also, chaos ensued as passengers at Bay didn't know which platform their next train might end up on, causing people to wait on the stairs. Switching trains also didn't add that much more time to a commute, of which the margin was further shrunk by the fact that at a rider's original stop they would have to wait for a correctly-bound train. Interlining was discontinued because of the confusion and delays, although many argue that it was politically motivated and that the experiment was sabotaged by the TTC, designed to fail from the start. Much of the infrastructure for interlining is still present on the system; most older stations still have changeable signs informing passengers of each train's next destination, though they no longer change.
Lower Bay is now used to train new operators, allow trains to change lines, for platform-surface experiments, and for various filming projects. The station has been modified several times to make it look like a "common" North American subway station.
The tracks connecting Lower Bay are still in existence and in use from time to time. They can be accessed northbound from Museum, turning right at the junction where the train veers to the left toward St. George. An alternate, albeit more unconventional route when travelling on foot, is westbound from Bloor. It has acquired a legendary status amongst so-called urban explorers, who often brave a host of dangers to gain access to the now-abandoned station.