That's the rapid transit division's work locomotive 04443. Lives at the Red Line maint facility at Cabot Yard, right across the tracks from the Amtrak yard and the South Station leads:
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50-ton, 700 HP, built 1987 by Plymouth. And has its wheel profile ground for running on the tracks of the 4 MBTA rapid transit lines, so it isn't used for commuter rail maintenance at all. I'm not sure how they transport it between the Red Line and Orange, Blue, etc. when it has to do heavy work elsewhere. There's no interconnections between rapid transit lines, or any currently active interconnections between the rapid transit lines and adjacent commuter rail lines. So they must be they must be able to transport it on a flatbed truck without too much trouble in order to get it between one point in the system and other.