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Phaedus had a iron- age civilization that was comparable to Earth's Roman Empire. In 2239, the Federation sent the Starfleet starship, USS Enterprise under the command of Captain Robert April and his first officer Alexander Marcus to do the first survey of the planet. During the survey, they saw that a genocidal civil war was being started the Shadow Phaedans. During the conflict, the Shadow ate and enslaved the children. (TOS - Countdown to Darkness comics: "Number One", "Number Two")
Captain April decided to violate the Prime Directive, fake his death, and help the oppressed Phaedans fight the Shadow Phaedans, to save them from extinction. For twenty years, April helped the oppressed Phaedans fight the Shadow by giving them Starfleet technology acquired by a trader named Mudd that was covertly supplied by Section 31 agents. During that time, April learned that the Shadow was supplied with weapons and technology from the Klingon Empire. (TOS - Countdown to Darkness comic: "Number Two"; TOS - After Darkness comic: "Part 1")
Starfleet agent "John Harrison" was dispatched to the system and discovered increased Klingon activity on the world. This was one of Harrison's final assignments before going rogue. (doc|Top Secret Security Review)
In 2259, Christopher Pike assigned the USS Enterprise to conduct a study of the world. A shuttle with a landing party was shot down by the Klingon weaponry, at which point its crew made contact with Captain Robert April. April explained the situation to James Kirk, particularly how Phaedus IV was a proxy war between the Federation and Klingon Empire, but Kirk refused to help. After an attempt by April to commandeer the new Enterprise, April was placed in custody of Starfleet Security however Kirk started to question the Prime Directive. Phaedus then became part of the Klingon Empire. The next year, Kirk met with April who accused Kirk of condemning the non-Shadow Phaedans to death. (TOS - Countdown to Darkness comics: "Number One", "Number Two", "Number Three", "Number Four", TOS - After Darkness comic: "Part 1")