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Memory Alpha

A protocol or procedure was a way or means of following established rules or guidelines in governing official affairs.

According to Tuvok, "a starship cannot run without protocols." (VOY: "Learning Curve")

The Federation's Prime Directive was recognized as its "cardinal protocol". (VOY: "Counterpoint")

Captains Rudolph Ransom and Kathryn Janeway both had differing opinions how they ran their own ships, the USS Equinox and USS Voyager while stranded in the Delta Quadrant during the 2370s. After Janeway noted that Ransom's crew addressed him by his first name, he explained that "when you've been in the trenches as long as we have, rank and protocol are luxuries," adding, "besides, we're a long way from Starfleet Command." Janeway, however, felt the opposite, stating that "I find that maintaining protocol reminds us of where we came from and hopefully, where we're going."

Later, when it came time to determine the protocol of who held seniority in their situation of "two Captains and two ships", Janeway cited Starfleet regulation 191, article 14: "In a combat situation involving more than one ship, command falls to the vessel with tactical superiority." In the case of the Equinox and Voyager, Voyager held that superiority, and therefore for Janeway protocol recognized her authority. Ransom, however, argued that "that protocol was written in the Alpha Quadrant. I'm not sure that it makes much sense out here," but Janeway held firm, stating, that "the regulation stands." Ransom seemingly obliged, "who am I to dispute protocol?"

Later still, Ransom cited Starfleet regulation 3, paragraph 12 – for his justification for killing nucleogenic lifeforms – "In the event of imminent destruction, a captain is authorized to preserve the lives of his crew by any justifiable means." Janeway disagreed with Ransom's reasoning, opining "I doubt that protocol covers mass murder." (VOY: "Equinox")

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