This protocol is only known to Starfleet captains. It gives them absolute power.

 All Trekkies know that the Prime Directive is the foundation of the Federation’s moral and ethical compass. This directive, above all else, is the one that Starfleet leans on. This rule is the guiding principle for all Starfleet personnel.

The fifth season of Star Trek: Discovery introduced a new protocol called the Red Directive, which seems to conflict with the ideals of the Prime Directive. It gives captains a lot of leeway to do whatever it takes to get the job done on red classified missions.

However, this isn’t the only Federation directive that conflicts with the Prime Directive. Star Trek: Voyager was the first to throw a galactic wrench in the Prime Directive when it revealed the Omega Directive. It doesn’t just conflict with the Prime Directive; it outright supersedes it.

Stranded in the Delta Quadrant, Captain Janeway and her crew are on a hundred thousand lightyear journey back to the Alpha Quadrant while never diverting from the principles of Starfleet; even in the most challenging of circumstances, they stuck to its principles—seeking out new life and new civilization, and, specifically, non-interference in pre-warp societies. This is the Prime Directive, also known as Starfleet’s General Order 1. Yet, all of this took a back seat to a secret mandate that only Starfleet captains are aware of.

Now, Starfleet officers aren’t strangers when it comes to violating the Prime Directive. And at times, we’ve come to expect that. Star Trek: “The Original Series” has had its fair share of violations of General Order One. And almost all of them involve Captain Kirk saving some civilization from itself.

In Starfleet, violation of the Prime Directive usually come in the form of some a moral dilemma.

Even the more “enlightened” The Next Generation violated the Prime Directive on occasions as well. One incident in particular—Data, of all Starfleet officers—had a run-in with General Order 1. In Season 2, Episode 15, “Pen Pals,” Data befriends a young alien girl from a pre-warp civilization, leading him to a moral dilemma about whether to save her planet from an ecological disaster.

Other violations are incidental. In Voyager Season 6, Episode 12, “Blink of an Eye,” the ship becomes trapped in orbit around a planet where time moves rapidly and inadvertently affects the planet’s civilization over centuries.

Some are a little of both. In Star Trek: Strange New Worlds, season 1, episode 1, Captain Pike violated General Order 1, hoping to correct Starfleet’s inadvertent contamination of a world. During Starfleet’s battle with the artificial entity in Discovery, season 2, episode 14, the battle took place less than a light year from a pre-warp civilization, enabling their scientist to gather data.

From the data, they created a warp bomb. In an effort to save the inhabitants from themselves, Pike, “reminiscent of TOS, revealed the Enterprise in dramatic fashion, hovering above the city.

Star Trek Voyager season 4, episode 21, titled “The Omega Directive,” introduced us to this protocol. The episode starts with the voyager suddenly dropping out of warp after the ship’s sensors detect a rare and highly dangerous molecule known as Omega.

This triggers an automatic, top-secret Starfleet protocol within the ship’s computer—the Omega Directive—rendering even Chakotay’s command codes ineffective. Captain Janeway is alerted to the situation, enters the bridge, removes the alert, and orders all the data sent to her ready room and the bridge crew to not discuss this with anyone outside of the bridge.

However, due to their unique circumstances—stranded in the Delta Quadrant—Janeway has no choice but to tell the senior staff about the directive. She briefs them on Starfleet’s top-secret protocol dealing with the Omega molecule—the most powerful substance known to the Federation.

The molecule has the potential to wreak havoc on subspace, rendering warp travel impossible, which makes its containment or destruction a top priority, even if it means tossing the Prime Directive out of the nearest airlock.

After some investigation, they trace the source of the Omega molecule to a space-faring civilization. This is where an important scene between Janeway and Tuvok takes place, underscoring the significance of the Omega Directive.

In this scene, Tuvok, in that stating-the-obvious Vulcan manner, pointed out the impending violation of the Prime Directive: “Captain, I’d be negligent if I didn’t point out that we are about to violate the Prime Directive.” Janeway’s response is shocking. She responded, “For the duration of this mission, the Prime Directive is rescinded.” Notice her choice of words here.

Janeway doesn’t say the directive is “suspended”—a temporary pause, suggesting a return to normalcy. No, she says “rescinded,” as in annulled, as if it never happened or existed at all. She’s literally saying to Tuvok, “Within the context of this current mission, when it comes to the Omega Directive, the Prime Directive does not exist at all.”

This isn’t just bending the rules; it’s show that when it comes to the Omega Directive, the Prime Directive isn’t just on the back burner; it’s off the stove entirely. There was no moral dilemma with Janeway—no right or wrong, no issue about upholding the principles of Starfleet—just destroy the molecule by any means necessary.

The Prime Directive is more than just a guiding principle; it holds a crew and its captain accountable for their actions. and Janeway is a strong believer in that principle, as evident in the two-part episode titled Equinox.

When the Voyager crew encounters another Starfleet vessel, the USS Equinox, that is also trapped in the Delta Quadrant, they take a different approach to getting back home. The Equinox crew is killing and harvesting bio-energy from nucleogenic creatures just to enhance their warp drive, allowing them to travel 10,000 light years in two weeks.

Janeway goes to great lengths to remind the captain of his responsibility to the federation and its principles. To Chakotay’s growing concerns, she fired on the Equinox; she almost killed an Equinox crew member during an interrogation; she tractor-beams an Ankari ship to strong-arm their cooperation; and she relieved Chakotay from command for questioning her orders.

To stress how important the Prime Directive was, part one of Equinox was the cliffhanger between the fifth and sixth seasons.

Yet, when it comes to the Omega Directive, there is no action that is off-limit. It gives any captain the license to pretty much do anything to get the job done—destroying the omega molecule.

In the final episode of Discovery season one, Commander Burnham gave a speech at a medal ceremony, reminding Starfleet of its principles: “We will not take shortcuts to the path to righteousness. No, we will not break the rules that protect us from our basic instincts. I am guilty of all of those. We have to be torchbearers, casting the light so we may see our path. We are Starfleet. That is who we are.”

The entire speech rings hollow in the face of the Omega Directive, and yet it shows that even in an institution like Starfleet that’s based on a high moral philosophy, there are still tough, morally ambiguous decisions to be made.

Voyager season 4, episode 21, sums up the complex rules and regulations Starfleet and the Federation have to juggle. The Omega Directive’s challenges the principles of Starfleet’s. It pushes the boundaries of what we thought was an unbreakable rule, although Captain Kirk would disagree.