What happened
Khrushchev protested that Washington was making an ultimatum. Strategic Air Command increased its readiness to DEFCON 2. That alert applied to SAC; it should not be described as a uniform condition for every American force. Naval pressure had still not removed the missiles already in Cuba.
Sources for this passage: [1] [2] [3]The barrier at sea and the strategic alert
The quarantine came into effect, bringing the possibility of a direct encounter with Soviet shipping. Khrushchev rejected the American action as an ultimatum. Some Soviet vessels halted or changed course, but this did not establish that work at the Cuban missile sites had stopped.
Strategic Air Command moved to DEFCON 2. Its bombers, tankers and communications belonged to a worldwide nuclear posture, separate from the ships enforcing the quarantine. The distinction explains why a seemingly limited maritime operation carried consequences far beyond the Caribbean.
Sources for this passage: [1] [3] [2]