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Project Pharos was a Starfleet operation to build a huge lighthouse on a planet in the Marrat system to broadcast navigational data to all vessels in the Marrat Nebula, and chart and log illegal traffic in the hopes of bringing order the Marrat region.

The project saw opposition from other species and states in the region. Local criminal elements fearful of Starfleet's impending ability to curtail their activities responded by raiding Starbase 13, the Starfleet facility charged with law enforcement in the area, and the base of operations for Project Pharos engineers. These attacks were made all the more deadly by the behind the scenes work of the Klingon Kaaj who brought about a pirates alliance of Arcturan, Khodini, Orion and Human forces. Kaaj suspected Pharos was the start of a Federation attempt to seize control of the Marrat Nebula, and after rallying the brigand forces attacked the Pharos siteworld.

The increasing hostile actions against Starbase 13 prompted Starfleet to call in the USS Enterprise. When, after Kaaj's attack contact was lost with the Pharos engineering teams, the Enterprise was sent to investigate and soon found itself under attack from Kaaj's ship the IKS Varchas. After a brief battle Captain Pike of the Enterprise was faced with the possibility of war with the Klingon Empire; to prevent this he resorted to radical tactics, targeting the Enterprise's phasers on the dilithium rich Pharos siteworld. The phaser fire ignited a chain reaction that engulfed the planet. The result was the destruction of the Pharos lighthouse, but the creation of a huge beacon in the nebula, achieving many of Pharos' navigational aims. (EV comic: "The Fires of Pharos")