The bodies were found near the Sutter Ave-Rutland Road station around 7:15 a.m.
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Preliminarily, they appear to be adult men but the remains are in very bad condition.
Law enforcement says the victims could be two graffiti artists from France, as the tunnel is a known graffiti location.
Two French passports were found at the scene.
It is likely these people were struck by another train, not the train that stopped, which was a northbound 3 train.
The motorman on that subway spotted the bodies and apparently stopped the train.
As a result, there was extremely limited 3 train service between New Lots Avenue and Crown Heights-Utica Avenue while NYPD conducted an investigation at Sutter Avenue and Rutland Road.
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Service alerts were resolved by Wednesday afternoon, though more information has not been released about the victims.
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