It seems like most of the people who wrote reviews of 999: Nine Hours, Nine Persons, Nine Doors thought very highly of it. I'm not sure why that was; I found the game to be a fairly tedious exercise in the repetition of insufficiently interesting puzzles. 999 creates this problem for itself because of its structure. The enforced replays that are central to 999's design and fiction ask for more from the puzzles and dialogue than they are able to contribute as art or entertainment. In addition to that, I felt that 999 had a tendency to undermine its plot and atmosphere during its moments of exposition, because it did not make proper use of the communicative elements on hand.
If you believe what the game tells you, 999 is a pressure-cooker of a story. Nine people have been trapped on a boat, with only nine hours to live if they can't find their way through the puzzles hiding behind nine locked doors. Part of the boat has already flooded, so the danger is palpable. In addition, there are signs from rather early on that one of the characters is the mysterious person who trapped them all in this situation. The actual gameplay has no time limit; 999's puzzles can be solved at the player's leisure. As such, it's up to the narrative elements to sustain the tension that the game claims is present.
999 stymies itself in this effort because its characters have a tendency to go off on long, rambling tangents that just aren't consistent with the idea that these characters believe they're in danger. In one instance, the player's character Junpei gets trapped in a freezer along with two others. The game tries to sell this as a threatening situation, but while the characters search for some means of escape, a conversation about the physical chemistry of carbon dioxide breaks out, followed by another little dissertation on the subject of ice-9. To the game's credit, Junpei can express some dissatisfaction with the way his companions are carrying on, but this does little to stop the unrelenting exposition.
This isn't to say that this dialogue sequence just couldn't work at all. Given that there's a situational hook for this conversation, it's much like expository scenes that play on TV or in books all the time. What differs in these cases is the context. In a television show, for instance, the characters would be searching through the shelves of the freezer at various points in the conversation, emphasizing that all the talk about sublimation is idle chatter undertaken as the characters are doing something else. In this case, the visual elements of the scene provide context that makes the conversation seem natural rather than weird.
In a book, the absence of context can be used to the same effect. In the case of a purely textual experience, the reader can be relied upon to create the parts of the scene that the author has left empty. With the help of a few sentences here and there indicating action, the reader will "fill in" the action as suits his taste. In fact, great writing is often as much about creating the ambiguous hooks for that sort of interaction as it is about being clearly descriptive of events and locales.
But 999 isn't a television show, and it isn't a book. It's a visual novel, combining graphical elements with text elements to tell a story. This combination is why so many of its tangents don't work—as I mentioned above, text and moving pictures support such digressions in opposite ways. A novel works by leaving the reader space to imagine the action, while a film works by showing the action. 999 feels like it's trying to be most like a book. However, the images of the speaking characters that accompany the text dialogue place constraints on the player's mental picture of the situation. The passive poses they adopt seem to define the action. Because of this, the situation feels like one where the characters are standing around casually discussing ice-9 while they're freezing to death in a meat locker.
This kind of problem doesn't happen all the time. In one of the puzzles, Lotus, a strangely dressed computer whiz, makes small talk as she's trying to hack into a PC. The screen shows Lotus typing at the computer, with Junpei looking over her shoulder, providing a visual context that makes sense of the conversation. Additionally, the written dialogue is accompanied by the sound of keys being tapped. Here, the audiovisual information provides just enough detail to enrich the depicted situation, without providing so much constraint that the player is forced to imagine something unsatisfying about the way things are happening.
Not every conversation in the game can be fixed by applying the approach from this positive example, unfortunately. Like many games, 999 drags itself out because characters who know they don't have much time to speak inexplicably refuse to get to the point. Also, some of the tangents are so irrelevant or redundant that they deserve nothing better than the knife. The ethylene diamine tartrate story, for example, is so much like the glycerol story that it adds nothing to the game besides a meaningless delay.
The fundamental problem for 999: Nine Hours, Nine Persons, Nine Doors and similar visual novels is that the graphic elements can define the action in a way that undercuts the story being conveyed by the text. In this case, the static portraits make the long segments of expository dialogue feel like places where everyone stops what they're doing to have a conversation, even though the situation being depicted is one in which the characters must advance through the ship or die. No matter what, these conversations would have been digressions. Had the developers used the visual elements more carefully, however, they would have helped sustain the tension rather than puncturing it.