A flawed masterpiece.
The centerpiece here was the brilliant story, but the way it was conveyed to the player is the issue - the logs had numerous spelling and grammar errors, and a large number relied on the player finding them in the correct order, which (as it did in my case) might not necessarily happen. Early on, this resulted in a bit of incredulity as to the quality of the story, and later, once the story has hooked the player, the way some information was simply missing depending on the route I took was a bit off-putting.
The simplistic graphics really aren't a problem for me, particularly given this was made for Ludum Dare, but the other major issue with the game was the lack of any kind of map screen, or even ability to place yourself in the ship. This resulted in a lot of frustrating backtracking and running in circles, occasionally going down the same passage numerous times in a row unintentionally. This could either be fixed with a basic map screen, indicating the player's position as well as the position of important locations, such as the storage door, the cockpit, the escape pod, the greenhouse, etcetera, or with a sort of 'in setting' navigation system, with lines of a partiuclar colour running from the cockpit to each section. For instance, a green line could run from the cockpit to the greenhouse, or a blue line from the cockpit to storage.
If you were to return to this to create a more polished version, this is what I would do:
Add two screens - a map screen accessible via M, and a log screen, accessible via L. When the Captain encounters a log, the log is removed from the world, and an entry is added to the log screen. The combination of these two features would allow the player to more easily navigate the ship, as well as access earlier logs for reference, and hunt down the logs they're missing by exploring parts of the map they haven't accessed yet.
I particularly liked the way the game simply ends when you open the storage door. I'm not going to spoil it for your other players, but I'm pretty sure I know what was on the other side.
All in all, this was fantastic. The issues I mentioned were stumbling points, but I was too engrossed by the story to really care all that much. I'd love to see more story-based stuff from you - once you get a proofreader, of course ;)