The Apocalypse

In Supernatural, the Apocalypse is started when The 66 Seals that bind Lucifer are broken and he is freed. The first seal is broken when a righteous Man sheds blood in Hell; Dean ends up breaking the First Seal when he spills the blood of a human soul in Hell. The Last Seal by was broken by Sam when he kills Lilith. Many angels including Zachariah intended for the End Days to happen. They believed that this would give Michael the opportunity to kill Lucifer. It is implied by both Castiel and Zachariah that Dean will stop Lucifer, this is later clarified - it is in his role as Michael's vessel that he can stop the Apocalypse. Four Horsemen of the Apocalypse and the Croatoan Virus are part of the demonic plan to cause death and chaos on Earth.

According to the vision of the future that Zachariah gives Dean in 5.04 The End, the intended trajectory involves the Croatoan Virus as a key part in the elimination of humanity. Apparently in 5.04 The End, all of Heaven bailed and left Earth to rot, for they probably thought Lucifer's end game was successful (Croatoan virus), and than decided that it was too late from them to win. In the present the Croatoan virus was released. However this Virus didn't infect the entire World as it did in the 2014 future. Pestilence played an enormous role in eliminating Humanity. However, he was permanently neutralized by Castiel.

Zachariah may have given Dean a false prediction of 2014. This was proven in 5.22 Swan Song. Due to the circumstances that were reveled in episode 5.22 Swan Song, we could be led to believe that Zachariah did in fact give Dean a false vision of 2014. 5.04 The End and 5.22 Swan Song had two very different outcomes.