As a narrative begins to unfold the writer's choices of motivations and settings will ultimately dictate the atmosphere of the piece.
There are a multitude of avenues for an author to indirectly reflect the atmosphere within a piece whether it is the mental state of the characters, the state of an environment or just a consistent pressure on the characters through events. The atmosphere of a narrative can determine whether the narrative is a page-turner or a casual read.
The mental state of a narrative's characters can be instrumental in establishing the atmosphere in a story. Viewing the world through the eyes a character with a bleak outlook will inherently bring an oppressive and dark atmosphere to the narrative. Just as well, a character that is unstable can add a sense of instability and uncertainty to the piece.
The choice of settings and the general state of those environments can serve to engross the audience with an almost palpable atmosphere. Are the characters interacting at a casual coffee shop that easily vanishes into the background? Visiting the standard fare of iconic landmarks? Settings that only serve as a stage for the scenes and easily vanish into the background. Or are your characters in a weathered old boathouse? A secluded small town locked away in the wilderness? Environmental settings that add to the overall tone.
Events within a narrative follow a steady rising flow like a wave that will eventually come to crashing end with the audience. It's the intervals of those events that can determine the pressure on the characters. A lengthy space between events can create a strong tension while short spaces and rapid pacing can establish a sense of urgency.
The strongest examples of indirectly building atmosphere include Neil Gaiman's Neverwhere, Stephen King's The Shining, Dean Koontz's Phantoms and even TV shows like the X-Files or Twin Peaks. Each of these excelled not only because of design but the subtle and indirect approach to building atmosphere.
Establishing an atmosphere directly can be extremely difficult based upon the chosen genre. In many Urban Fantasy pieces the author will choose dark settings and lace the story with numerous deaths but the atmosphere seldom rises to consume the piece and envelop the audience. In most instances it is a failure for the events to have a sense of weight. In many instances of directly establishing atmosphere it almost always depends on the overt setting.
The atmosphere of a narrative should be almost palpable. It should consume the audience to the point that they feel they are living in that world.