There are so many things I like about the game… the tutorial is great (brief, and to the point), shooting enemies is fun, the white/green colour contrast, the final battle with all your comrades.
However, I'm not sure about the story… it feels like I'm missing something. The dialogue at the beginning made it seem like there's a mystery to uncover – but in the end, it's just ‘kill the big bad guy’. The reason might as well be running out of time because of the game jam… but I wouldn't exactly call the ending ‘a satisfactory conclusion’. But the gameplay is pretty good nevertheless.
Edit:
Thank you for clarifying the story. I got that pandemic analogy and the importance of team effort in the end, but as for the rest… I think the main thing which undermines the "alone, hopeless" feel is the radio communication throughout the game. You're constantly talking to an authority figure who is comforting you – so you're feeling neither completely alone nor hopeless.
Imagine this: the main character doesn't have anyone to talk to, the radio is silent (in truth, you're too deep underground to get any signal). He fears he might be the last person on Earth. In hopes of leaving at least some legacy, he records his thoughts on tape (so you can basically keep saying the same things which he already says in the game).
He goes further, but there's no improvement, the enemies only get stronger. Then he runs into "the main boss" and thinks he's done for, but suddenly, reinforcements appear and you defeat it together.
At least that's how I'd go about it if I wanted to make the player feel lonely or depressed until the very end.