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Counter Strike was an organization of aliens, who came from the same mysterious species as the Aegis. Like the Aegis Counter Strike monitored the growth of other civilizations. However, unlike their cousins, Counter Strike was a malevolent organization, and when they deemed a civilization to have developed too far and/or too fast they struck out, and violently halted their progress.
For centuries Counter Strike swept the galaxy destroying worlds they considered too advanced. But some worlds resisted; through greater wisdom, like the Vulcans; or through pure military might, fighting back at Counter Strike's attacks. And so Counter Strike eventually altered their tactics becoming more subtle in their subversive way - giving certain species highly destructive technology, so that they might destroy themselves. (TOS - Assignment: Earth comic: "We Have Met The Enemy...")
In 1968 Aegis Agents 201 and 347 found evidence indicating Counter Strike may have been responsible for the Nuclear warhead platform about to be launched from McKinley Rocket Base. The two agents decided to make an encrypted record of their findings which would eventually be found on their Beta 5 computer if anything happened to them. A fortunate precaution as the two agents were rammed off the road en route to the base in a less than accidental automobile incident.
Supervisor 194, aka Gary Seven, was sent to Earth and completed the agent's mission to disable the warhead platform, but remained unaware of who was responsible for it. (TOS episode & novelization: Assignment: Earth)
Three and a half years later, and after Seven had thwarted several other unusually advanced technologies on Earth, Beta 5 decrypted the agent's records. Seven, and his assistant, Roberta Lincoln, proceeded to retrace the agents footsteps to investigate. Beta 5 was able to create a projection of the agents’ final movements, allowing Seven and Lincoln to witness their "accident" and prompting them to contact the local sheriff’s office to follow that lead.
When Seven asked about the accident he promptly found himself under attack by the police, who had been programmed by Counter Strike to respond to anyone asking about the accident. Counter Strike's involvement confirmed, Seven intended to return to his office to report to his superiors, but was shot before he could teleport. And before Lincoln could get him to safety they both found themselves transported aboard a Counter Strike starship in orbit of Earth.
Lincoln found herself face to face with a member of Counter Strike, and tried to use Seven's servo against it, but, as Seven informed her as he regained consciousness, it would not work there. The alien then took Seven by the neck, but released him moments later in a convulsive fit - Beta 5 could not teleport Seven and Lincoln out, but could send a disruption wave which knocked out the Counter Strike crew.
Seven armed himself with a Counter Strike rifle and began firing at the ship, aiming to take down the shields, and activating the ship's auto-defense system in the process. As mechanical arms began to grasp for them, Seven blew a hole in the ship's hull, blowing Lincoln and himself into space.
Moments later both found themselves aboard an Aegis starship, which took advantage of the Counter Strike vessel's downed shields and destroyed it.
Satisfied Counter Strike's efforts had been quelled the Aegis cleaned up the mess - clearing the memories of those brain washed by Counter Strike, and left Gary Seven and Roberta Lincoln on Earth to deal with whatever crisis would arise next. (TOS - Assignment: Earth comic: "We Have Met The Enemy...")