Was a bit confused at first (and I'm still not 100% on a few details) but on a second reading it really clicked and oh boy this was cleverly done.
I think others have already pointed out my primary knocks on this, which are:
1) Some missing polish on typos, dialogue sprites for Marcos, and other things like missing dialogue tags. In a story where most of the information delivery is subtle like this one, each detail can be extremely important so not knowing whether something was a mistake or an intentional decision can affect how you interpret what's going on. For example, the line "Don't patronize me Marcos..." seems like it's supposed to be spoken by Rafael, but with the tag missing I'm not sure whether that's an error or supposed to be Marcos' internal monologue slipping.
2) The middle of the story is a bit awkwardly paced. There are some lines and details that could probably be cut or adjusted, like the exchange about Rafael staying home and playing video games while Marcos works out. I can see where you might be trying to go with that by establishing how alone Rafael is/was/feels/felt, but you already set this up better elsewhere and this particular exchange doesn't really add much, especially past the halfway point in the script when things should really be starting to ramp up.
Spoiler warning (more minor than normal though, honestly) for the plot from this point forward.
Pretty much everything regarding the central metaphor and the imagery surrounding that was fantastic - on second reading, it becomes much clearer how brilliant the intro is at setting that up. As others have mentioned, the ways things begin changing in the background is really well done, some of which (the memories box) I didn't even notice the first time through, though toolbox smiley face is still definitely my favorite. This is my favorite kind of horror - the kind that makes you feel uneasy and gets under your skin rather than SPOOKYGHOSTFACE dopamine hits. Usually I'm not a huge fan of Owl Creek Bridge-type plots but the execution really sold this for me.
I'm not quite clear on a few things like what the "accident" was, what exactly Rafa's fate was between then and current events, and how those two might be related, but I can also see those being intentionally vague. Like I know the most important part is just that Marcos is consumed by his guilt, but maybe just another clue or two as to why exactly that guilt manifested would be helpful.
This was great work though and everyone on the team should be really happy with this one.
Final rating of 29 loops of the Sonic the Hedgehog tense underwater music out of 2 concrete shoes.