Let's set the stage:
The Amtrak Lake Shore Limited originates in Chicago and travels east to Boston. The train actually gets physically split in Albany, NY, with most of the equipment heading south to New York City and a few coaches, a baggage car, and sometimes a sleeper car (and obviously a locomotive!) heading east to Boston. Anyway, after departing Chicago at 9:30 PM the previous night, the Boston section of the train is due into Worcester every day at 6:44 PM. It then stops at Framingham and Back Bay before arriving at South Station at a scheduled time of 8:01 PM. This train has the unfortunate nickname of "LATE Shore Limited" since it is very frequently delayed.
On Wednesday night it was not only somewhat late - probably about an hour - but it also became disabled just east of the Worcester station. Unfortunately the Worcester station only has one platform, and the Amtrak train must have broken down in a location that blocked MBTA trains from approaching the station.
Outbound MBTA train P533 is due to arrive in Worcester at 7:40 PM. It is then scheduled to head back into Boston as inbound P536, scheduled to depart at 7:50 PM.
Around 7:50 PM, the @MBTA_CR twitter feed started to notify passengers that P536 would be delayed departing Worcester due to the disabled Amtrak train. Eventually, the @MBTA_CR feed notified passengers that P536 would originate at Grafton - and GPS data indicated that the P533 / P536 equipment had never made it to Worcester on the outbound trip, presumably due to the disabled Amtrak train.
Meanwhile, outbound P535 was due to arrive at Worcester at 8:17 PM and head back into Boston as P538 with a Worcester departure time of 8:30 PM.
This P535 / P538 set eventually shoved the disabled Amtrak set BACK westbound into the Worcester station, where passengers (including @emmalineJen) were directed to board the MBTA P538 equipment relatively far up the platform (to the east) as the crew finished coupling the two sets together.
By this time, P536 had made its way back out to Grafton, where GPS data showed it stopped at the Grafton station for a very long time. It only departed Grafton after the departure of outbound P537 on the opposite track. This may explain how Worcester bound passengers on P533 (which became P536) were able to get to Worcester. Since that P533 / P536 equipment was never able to get to Worcester because of the disabled Amtrak train, the P533 Worcester passengers remained on the train until they were able to transfer to outbound P537 at Grafton.
At about 9:00 PM, the double draft Lake Shore Limited - MBTA P538 combination train departed Worcester, presumably carrying passengers from Chicago, Cleveland, Upstate New York, and MBTA passengers intending to take both P536 and P538 towards Boston. The P536 Worcester passengers were delayed about 1 hour and 10 minutes while the P538 passengers were delayed about 30 minutes.
The extremely long delay for Worcester originating P536 passengers (and Worcester bound passengers from P533) could presumably have been prevented if Worcester had two platforms and two tracks for passenger trains to service. But even that isn't guaranteed - it is possible that the Amtrak train was in a position that blocked all access west of CP 44 or CP 43 (see the map). Implementing two platforms at Worcester is somewhat difficult due to the freight yard immediately across from the station, but there is space to re-establish a center platform between the current station track and the next closest mainline track. I have heard that it is a long-term goal for the MBTA to restore that center / 2nd platform, but we all know that the MBTA does not have tons of spare cash lying around to knock out capital projects here and there. Maybe someday...