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A modern locomotive essentially consists of a big diesel generator connected to some electric motors. In principle, there's no reason you couldn't replace the generator part with a bank of batteries. This would suck for long-distance hauling, but for things like the MBTA commuter rail, where many of your trains spend non-rush-hour just sitting around, it seems like it might work. If you have a 200-mile range and can charge in six hours, that's almost good enough to do two rush-hour round trips on the line of your choice, though without much safety margin. Since you know where both ends of the line are, you can build a smallish number of charging facilities where your trains lay over.
Googling for "battery locomotive" gives some hits. If you're working in a mine, it seems to be the way to go, but those are specialized devices, and clearly not quite up to FRA regulations for railroad use. UP also has a battery-powered switching engine but it doesn't go faster than 20 mph. 2,000 horsepower feels a little underpowered, but I don't know how much power you actually need; all of the T's current locomotives generate 3,000 HP, and one engine is enough to run a long double-height south-side train, so a smaller engine might still work for things like five-car single-height Haverhill trains.
Googling for "battery locomotive" gives some hits. If you're working in a mine, it seems to be the way to go, but those are specialized devices, and clearly not quite up to FRA regulations for railroad use. UP also has a battery-powered switching engine but it doesn't go faster than 20 mph. 2,000 horsepower feels a little underpowered, but I don't know how much power you actually need; all of the T's current locomotives generate 3,000 HP, and one engine is enough to run a long double-height south-side train, so a smaller engine might still work for things like five-car single-height Haverhill trains.