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An exotic fungus destroyed most of the colony's food supply, leaving the colonists, of which there were eight thousand, in serious danger of starvation. Governor Kodos made a drastic decision: he ordered the deaths of four thousand colonists, so that the other four thousand might live, selecting those to be killed according to his personal theories of eugenics.
Supply ship arrived earlier than expected, but too late to save the four thousand people. All they found of Kodos was a burned body, and he was presumed dead, until his chance discovery on Planet Q twenty years later.
The outbreak of the war was marked by the Battle of the Binary Stars. This battle was provoked by T'Kuvma, a Klingon from the House of T'Kuvma, to rally the Empire to a common cause as he had portrayed the Federation as an existential threat, whose space had encroached unacceptably close upon that of the Klingons. In the first six months, the Federation lost 8,186 people.
The USS Discovery, with its Spore Drive, provided a crucial, albeit covert, advantage for the Federation. After T'Kuvma's death, the unified Klingon effort fractured. The war ended with a truce, partly due to the Klingons being divided. L'Rell, a follower of T'Kuvma, used a Federation-planted bomb on Qo'noS to seize power, unify the Empire, and secure peace.
After a century of isolation, the Romulan Star Empire engaged in a series of unprovoked attacks on several outposts along the Neutral Zone. During the incident, the first visual contact of the previously unseen Romulans themselves are made, revealing them to be an offshoot of Vulcans. The Romulans used the Neutral Zone as a testbed for a couple of new technologies, such as a cloaking device and a new type of energy weapon, and how these would serve them in a second Earth-Romulan War.
The Romulan Commander, Keras’ mission was almost successful; however, the USS Enterprise discovered and attacked them. Despite the use of plasma torpedoes and the cloaking device, Keras's ship was crippled. Instead of surrendering or facing capture by Starfleet, Keras engaged the auto destruct, destroying himself as well as his vessel.
This defeat dishonored Keras's House and stopped further Romulan expansion for some time.
Ongoing negotiations between the United Federation of Planets and the Klingon Empire started to breakdown. Starfleet Command expected that the Klingons would launch a surprise attack after they issued an ultimatum demanding that the Federation withdraw from all disputed regions along their mutual border. When the Federation refused the demands, the Klingons launched an immediate attack, even before an official declaration of war was issued.
The USS Enterprise was ordered to the planet Organia, which occupied a strategic location in disputed space (now the front lines of the war). Captain Kirk's orders were to prevent the Klingons from occupying the planet and using it as a forward base. At the time, the Organians were believed to be a simple, pre-warp agrarian society. Kirk and Spock beamed down to offer the Organians assistance in defending against the impending Klingon attack but they refused. Minutes later the Klingons invaded, Commander Kor proclaimed the planet a new territory of the Klingon Empire, with himself as military governor.
The Enterprise was joined by a Federation fleet, and were about to engage the Klingons in battle when the Organians, not wanting anymore violence, revealed themselves to be extremely advanced noncorporeal beings. They altered the perceptions of all Federation and Klingon ships, and soldiers, making it seem as if weapons and instruments of war were suddenly too hot to touch. In this way, they brought about an abrupt end to the war.
They appeared to both the Federation Council and the Klingon High Council and announced the unilateral imposition of the Treaty of Organia, which established ground rules for further interaction between the two powers, and for the resolution of the territorial disputes.
The Romulans and Klingons forged a rare alliance, motivated by mutual hostility toward the Federation. The agreement included military cooperation and a major technological exchange: the Klingons provided the Romulans with D7-class battlecruisers, while the Romulans shared cloaking technology. Despite the initial promise of the pact, neither side fully trusted the other.
The alliance soon decayed as each empire realized that its strategic goals diverged and that any temporary partnership would ultimately benefit its rival.
First detected when passing through Klingon territory, V'ger launched a series of powerful, spherically-shaped "bolts" of plasma energy, vaporizing a fleet of three Klingon K't'inga-class battle cruisers. It then passed into Federation space near the Epsilon IX station, which it also destroyed.
With the entity being over 54.3 hours from Earth, Starfleet rushed the refit of the USS Enterprise, so that it could be launched in time to intercept V'Ger. After penetrating the huge entity and traveling to the center, Admiral James T. Kirk and his crew encountered V'Ger, who proceeded to send a probe that "absorbed" Enterprise navigator Ilia; with all of her memories and personality. The probe returned in the form of Ilia.
Soon after, the Enterprise crew discovered that V'Ger was actually the NASA probe, Voyager 6, which had been launched from Earth in 1999, entered a black hole which transported the probe across time and space to another part of the universe, where it was encountered by an advanced civilization of living machines. These sentient machines turned it into a like member of their race, giving V'Ger sentience and sending it off to complete the mission which the once Voyager 6 was originally assigned to accumulate all knowledge and return give it to its creator.
Over the hundreds of years it took to return home, V'Ger took its mission to heart and learn everything it could to extremes, as it absorbed everything it was exposed to, and having learned everything, wanted to return to Earth to impart its knowledge and join with its Creator. Realizing that the fate of Earth was in their hands, Commander Willard Decker joined with the entity and programmed the information it needed to transmit its data. Once the two were joined, the entity evolved onto another plane of existence and headed for the Andromeda Galaxy.
In 2267, Captain Kirk left Khan and his followers on Ceti Alpha V in exile. Because Kirk never returned to check on their progress, he had no way of knowing that a catastrophic environmental calamity had occurred that made Ceti Alpha V a desert wasteland, just months after Khan and his followers were left on the planet.
22 years later, the USS Reliant was on a survey mission to find a suitable location for Project Genesis, a Federation project to turn an uninhabitable world into an M-class planet. While examining what they thought was Ceti Alpha VI, Captain Clark Terrell and his first officer, Commander Pavel Chekov, were captured by Khan and his followers. He implanted each with Ceti eels and learned not only why they had come to the planet, but also where he may find James T. Kirk. Shortly afterward, Khan and his people took control of the Reliant, marooned the crew on Ceti Alpha V, and set out to get revenge on Kirk.
Khan intercepted the Enterprise, which was en route to Regula I. Concealing her intent, Reliant approached, feigning communications trouble, and mounting a devastating surprise attack on the Enterprise. The ship was eventually able to escape and went into the Mutara Nebula. Reliant pursued Enterprise and the two ship fought. At the conclusion of the battle, Reliant was defeated, However, Khan detonated the Genesis device in a final attempt to kill Kirk and destroy the Enterprise. Fortunately, the Enterprise escaped thanks to the sacrifice of Captain Spock.
The first Federation ship to encounter the mysterious Probe was the USS Saratoga, which, like several other vessels, was disabled by its powerful transmissions. After reaching Earth, the Probe shut down Spacedock One and the Excelsior, then began transmitting into the oceans with such energy that it started evaporating seawater and disrupting the atmosphere, causing worldwide power failures.
The Federation President issued a distress signal warning all ships to avoid Earth, which was received by Admiral Kirk aboard the captured Klingon HMS Bounty. Spock deduced that the Probe’s signal was aimed at Earth’s oceans and resembled the calls of extinct humpback whales. He theorized the Probe had been sent by an alien intelligence that once communicated with whales and was seeking them.
Unable to destroy or approach the Probe, the crew concluded that only actual humpback whales could respond. Kirk decided to travel back in time, retrieve whales from 1986, and return with them to 2286. When the whales responded to the Probe’s call, it departed peacefully, restoring Earth’s atmosphere and returning power to disabled ships.
A catastrophic explosion on the Klingon moon, Praxis, cost the Klingon Empire their key energy production facility, as well as imperiling Qo'noS's ecosphere. Without diverting resources from their vast military expenditures to combat the disaster, the Klingon Empire had approximately fifty years remaining before it dissolved, according to Starfleet estimates.
Vulcan Ambassador Sarek directed his son, Captain Spock, to open a covert dialogue with Gorkon, the Chancellor of the Klingon High Council in the weeks following the disaster. Gorkon recognized the Empire's precarious state, and through Spock, he proposed immediate peace negotiations with the Federation. Officially, the Federation and Klingon Empire embraced Gorkon's peace initiative, and Gorkon departed for Earth aboard the battle cruiser Kronos One.
The prospect of an end to nearly seventy years of hostilities, coupled with massive demilitarization, was not welcomed by all. A cabal of disaffected officers from the Federation Starfleet, Klingon Empire, and Romulan Star Empire, formed to undermine the peace talks.
The USS Enterprise-A, escorted Kronos One on the journey to Earth. A prototype Klingon Bird-of-Prey, capable of firing her torpedoes while cloaked, shadowed the vessels and attacked Kronos One, while an accomplice aboard the Enterprise forged the databanks pertaining to torpedo magazines suggesting the Enterprise had fired. Lieutenant Valeris ordered Yeomen Burke and Samno to board Kronos One in the chaos, where they assassinated Gorkon. After Kirk and Leonard McCoy boarded the battle cruiser to offer aid, they were accused of murdering the Chancellor, arrested, and taken into Klingon territory for trial.
In spite of the conspiracy's efforts, the peace process continued between the President and Gorkon's daughter, Azetbur, and a summit was scheduled to take place at a secret location. Kirk and McCoy faced their show-trial, prosecuted by Chang. Though earnestly represented by Colonel Worf, the officers were convicted and sentenced to life imprisonment on the dilithium mines of Rura Penthe. Kirk found an "ally" in the comely Chameloid, Martia, who led the new prisoners to the surface and into a trap. Just before their attempted murder by the prison warden (another lackey of the conspiracy). Kirk and McCoy were rescued by the Enterprise.
Spock's shipboard investigation turned up the bodies of Burke and Samno, and exposed the treason of Valeris. Spock's forced mind meld with his erstwhile protégé identified the leading conspirators, and their new plan to assassinate the Federation President. From Captain Hikaru Sulu, they learned the location of the secret conference at Khitomer, on the Klingon border. Despite further actions by the cabal, the Khitomer Conference was a success.
It ultimately led to the signing of the Khitomer Accords and the beginnings of nearly a century of peace between the Federation and the Klingon Empire.