Warning: contains spoilers for Star Trek #6!V'Ger, the "villain" of the God City of T'Kon, awakened from a long slumber, is on a collision course for Earth - where it plans to destroy the planet. As the threat approaches, Starfleet mobilizes the fleet, and readers learn of the existence of the "V'Ger Protocols," created for situations just like this.
The text piece does not reveal the V'Ger Protocols in their entirety, but it does share enough details to see they're extreme. When the V'Ger Protocols are enacted, all ships are recalled and all missions canceled; the briefing singles out peacekeeping and research missions. These two types are extremely common for Starfleet vessels, so to suspend them speaks volumes to the wide-ranging nature of the V'Ger Protocols. The V'Ger Protocols are so dire that it takes no one less than the Federation President to enact them.
Starfleet's V'Ger Protocols Are Extreme
Star Trek made a triumphant return in 1979 with its first full-length feature film, and the crew of the Enterprise were given a movie-sized villain in V'Ger. The movie begins with V’Ger destroying three Klingon ships, and Starfleet learns it's on a direct course for Earth. Kirk and the Enterprise intercept the alien, and learn the truth of its origin: it was once a Voyager satellite that had fallen into a black hole. It emerged in a distant sector of the universe, near a planet of machine beings.
Seeing a kindred spirit, the machine aliens refitted the Voyager probe, creating a vast vessel to contain it. They then sent it back to Earth, its home. Kirk and company were able to reason with the alien; it merged with two Enterprise crew to form a new life-form that promptly left our plane of existence. While V'Ger is long since gone, it modeled a threat that Starfleet was not ready for at the time - but now that has changed.
Starfleet Is Prepared for the Next V'Ger
While Sisko and his crew are able to stop the God City of the T'Kon, Starfleet is clearly ready for a V'Ger-level threat, and they'll have to be. The Klingon emperor Kahless is currently killing the franchise's godlike beings, and using their powers to enhance his weapon the God-Killer Array. Hypocritically, Kahless is now flirting with godhood, and it's clear that he sees Sisko and Starfleet as the only true threats to his ambitions.
When V'Ger attacked Earth in Star Trek: The Motion Picture, the Enterprise was the only vessel within intercept range; furthermore, the alien was able to disable Earth’s planetary defense systems. In short, Starfleet were caught with their guard down and V'Ger was able to nearly destroy the planet. Now, it's revealed that Starfleet has enacted a series of protocols in advance, but as Kahless undermines the fabric of creation, even these extreme measures may not be enough to handle Star Trek's new galactic threat.
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