The SM-13 starts breathing for Simon after he says he trusts it
I don't know if anyone's said this, or something very similar. Probably yes. But I was checking numbers on my last rewatch and paid attention to the oxygen timing, and wanted to put my thoughts in order.
I think the SM-13 had about 2 hours worth of oxygen total. And I'm basing this on the amount of time we get between the first light going down, and the next, where we have no (apparent at least) cut in time or montage of passage of time.
We get the first light going down at 00:07:32, when Simon first notices what's probably a tighter timing than he was counting on, or at least makes him aware of the passage of time. By this point we has a montage of him going through the ocean floor while the credits appear on screen, so I'm assuming it's safe to say that more time than 7 minutes has passed.
We can also see that in that time, he has made relatively little progress, but has made a little ways into the map per his marked path. About 30 minutes seems like a decent time for being welded into the SM-13, lowered into the ocean, and making a little ways down there while both familiarizing himself with the controls and how to navigate the landscape, and moving about the rover to both take pictures and mark his progress. At this point he seems to be taking things carefully.
Now, the next oxygen light goes down after we've followed Simon without any apparent cut, through finding the skeleton, being pulled up and dropped down, talking with David, and having a spat with Ava while talking about ramming the thing. This happens at 00:37:44.
So assuming each light represents an even time of amount of oxygen (which seems more likely), each light would have about 30 minutes worth of oxygen. Four lights, roughly 2 hours of oxygen.
Which fits for a recon mission getting to each point of interest, or as it was called, going down to take a few pictures and coming back up. Those trips weren’t really meant to take too long, or at least not without at least one stop to fill resupply the oxygen tank.
It'd also fit the lack of resources present in this universe. A ship meant for shorter missions would take overall less resources put into it.
And then we have Simon being pulled back into the blood ocean by Elli, and being cut off from the Tow Ship so it doesn’t go under with him. And he's lost in the blood ocean, known to mutate/change some things (and not necessarily strictly tied nearness to the Light, as Simon seems to start understanding Elli only after spending some time down the ocean).
Even assuming he doesn’t lose any time between blacking out and waking up, the third oxygen light should have gone down around 1:07:00-1:08:00. Which doesn’t happen. The next light goes down at 1:12:00, while he's talking to Elli, so roughly four minutes past when it should have (again, assuming the time on screen is the same as the time actually spent in universe, and that Simon wakes up quickly after pummeling down the rover). It's likely at least a little more time has passed.
But you know what happens in between that time? Simon saying he's trusting the SM-13 at 1:00:27.
In a story with themes about belief/understanding changing the world ("It thinks therefore we are"), and a line saying the ship is alive by the end of the movie as well as the fact Simon does survive longer than he should've down there, this seems to me like a good time to say the ship started truly changing.
That it starts breathing for its pilot after Simon places his trust and determination to live into the SM-13.
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