While pursuing Nina Myers in Mexico, Chase Edmunds saw a suspicious light and followed up on it. When Chase arrived at the destination, Nina held Chase at gunpoint, coercing him to announce a "Code 6" over the radio, presumably synonymous with "all clear."
During Day 5, Jack Bauer realized that Ostroff (whom he had just killed) planned to release a canister of nerve gas in CTU's ventilation system. Bill Buchanan immediately called for a Code 6 evacuation.
Due to the confusion caused by having called a lock-down right before, the facility was not properly evacuated, and about 40% of CTU's staff was killed due to the nerve gas.