Well I want to say that they were trying to cut into the rudder line in the battery compartments, because I'm pretty sure it was the location of the job to be done that brought up the concerns about hydrogen. There was a gauge that they kept looking at which showed the concentration, at one point the alarm for it went off and the needle was in the red zone, and the chief just turned the alarm off because there was nothing they could do about it. He checked that gauge before starting the job on the rudder line as well, and I'm pretty sure it was in the same compartment where they were working. I think he'd told the CO that hydrogen concentration was up to 17% at that point. Given how little was actually working on the boat, whatever was supposed to be keeping the hydrogen in check with regard to the batteries probably wasn't working either.
The scene of what happened just before everybody burnt up was of the one guy doing whatever he was doing to get the lights back on, and then a quick shot of what looked like a wire or tube glowing as it heated up. I'm assuming that this was another malfunction because why would anyone make that happen deliberately given the situation? Or maybe the guy opening the hatch from another compartment at just the wrong moment actually did figure into it somehow.
I did read that "hydrogen gas forms explosive mixtures... with chlorine in the range 5–95%. The mixtures spontaneously detonate by spark, heat or sunlight" but I don't remember them mentioning anything about chlorine being an issue at that point in the movie. And in fact I was kinda waiting for that, because I know chlorine leaking from batteries on a submarine is A Very Bad Thing.
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