On weekdays the last direct train to Warm Springs leave Civic Center at 7:11 p.m. . However the train to Dublin Pleasanton from which you can transfer to a Warm Springs train at Bayfair leaves the Civic Center Station as late as 11:55 for the last one.
Last to Fremont is like 1030pm last to east bay is Concord 1145pm
Check schedules online
You can always use the BART official app or look online for schedules but I'm pretty sure it's just before midnight. No trains between 12am and 5am.
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