The scientific and historical themes of the game are interesting, though not contributing as much to the plot itself, or probably serving as foreshadow for Virtue's Last Reward.
The endings system doesn't work in the best way, but it's still a exciting story to follow. A bit of verisimilitude, with a cast of charismatic characters, constant mysteries, and surprising resolutions. Puzzles and narrative events that will genuinely make you think and reason. It's well conducted and interwoven, and I believe, driven at a good pace. Perhaps VLR will cover all the remaining mysteries surrounding 999.