...any complicated system in nature, and that includes the Zone, automatically seeks equilibrium in the absence of destabilizing external factors. That was the case here in recent years - the Zone was stable and there were no significant deviations from the norm... And now? Now we've seen a gigantic emission that has changed the face of the Zone. The system became unstable, distorted... a glitch, of sorts.
Professor Beanpolev
The Second Emission is the key event which begins the Clear Sky story line.
Overview[]
The Second Emission (not to be confused with "Second Incident" that occurred in April of 2006) is known to be a massive psy-emission that occurred sometime in September of 2011. This coincides with the end of the first successful expedition to the heart of the Zone, which is the Chernobyl NPP. Previous to this, the only individuals to penetrate so deeply into the Zone were brainwashed into unwittingly performing C-Consciousness' will. This group is hostile towards outsiders and eventually became known as the Monolith faction.
The successful expedition was made up of three stalkers who went by the names of Strelok (the group leader), Ghost, and Fang. The group came very close to discovering the secret work of C-Consciousness. C-Consciousness' discovered the intrusion and triggers a massive emission known as the Second Emission as attempt to kill the retreating intruders.
This attempt was unsuccessful, as the group somehow survives the massive emission. Strelok's Group had a propensity for the underground and it's quite possible this is what saved them.
The Second Emission also sets the plot of the series' prequel game Clear Sky when Scar is leading a scientists group in the Great Swamps, survives the emission and is picked up by Clear Sky's Leader N.A. Lebedev just before getting eaten by pseudo-dogs.