The T and Keolis say Amtrak's signal system failed on the Northeast Corridor this morning, and since Amtrak and the T's commuter trains share some of the same tracks and stations, that led to massive delays and exhortations to riders that they just get off at Back Bay or JFK and ride the subway into town - with assurances their commuter-rail passes would get them onto the Orange and Red Lines.
A Keolis spokesman explains:
A little before 6 this morning, there was an systemwide Amtrak power failure, impacting inbound and outbound commuter rail service at South Station. Power was restored about an hour later. In the interim, because trains could not get into or out of South Station, passengers were switched to subway stops along their respective lines to keep their commutes going rather than wait for the issue to be resolved. Still, we have residual delays and train cancellations along some lines. 30-45 minute delays on average.