The project that resulted in the creation of this technology was the result of a top secret Federation scientific program which was intended to quite literally produce life from lifelessness.
When activated, it produced a type of radiation that was unlike any previously known. This energy field was called the Genesis Wave which was believed to be in phase with the basic structure of living beings. When the proper radiation level was reached, the Wave began altering the surrounding matter. This, in theory resulted in two effects the first of which was the creation of organic molecules as well as create primitive lifeforms such as vegetation and also prepare the target location to support carbon based life. This resulted in the development of a Class M world with its surface reshaped and terraformed with its elements restructured to support a living environment. However, when activated in the presence of existing life forms, the wave destroyed them and restructured them to match the new life matrix of the Genesis Effect.
The device was incorporated into a transparent/translucent torpedo casing which protected the delicate internal components from radiation, temperature increases and other adverse conditions. This made it capable of being launched from a specially designed mechanism and carried in a shuttle bay. Once activated, the torpedo casing which was where the device was located in built up to critical levels whereupon in 4 minutes time it began to affect matter near it. Referred to as detonation, this instantaneous reaction was even more destructive to matter when compared to a simple explosive. After it was unleashed, there was no way of stopping the Genesis Effect, even if someone destroyed the device itself. (FASA RPG module: Star Trek III Sourcebook Update)
Once impacting its destination, it triggered a massive explosion of energy which radiated from its location to encompass its entire impact region whereupon it reduced everything into subatomic particles. The pre-programmed matrix was then responsible for reassembling the subatomic particles into the desired configuration. This allowed it to create an atmosphere and appropriate environment that was habitable for Humanoids. All this was accomplished in a matter of hours with vegetation and other forms of life emerging on the planet or location the energies of the device was exposed to during the activation. (TOS movie, novelization & comic adaptation: Star Trek II: The Wrath of Khan)
The scientists responsible for the creation of the technology were not sure of the limits of the Genesis Wave with it being virtually capable of traveling through limitless distances as well as over and through matter which included gas but did not travel well through a vacuum. (FASA RPG module: Star Trek III Sourcebook Update)
Due to the capabilities of the device, Genesis was capable of being perverted into a powerful weapon. This was because whilst Project Genesis was intended for use on planets or regions without life, should there be any life in the designated area then the device would destroy it and recreate it to those that matched its matrix. (TOS movie, novelization & comic adaptation: Star Trek II: The Wrath of Khan)
The Genesis Device was programmed so that it could create an entire star system, complete with a main sequence star if needed, but was intended to only be used on a single dead planetary body. (TOS movie, novelization & comic adaptation: Star Trek II: The Wrath of Khan)
There was one problem within the original Genesis device which was later revealed by its co-creator who stated that in order to make the machine work, he had to use unstable Protomatter. This led to an instability which brought about the destruction of a planet that the machine had created. (TOS movie, novelization & comic adaptation: Star Trek III: The Search for Spock)
The concept of the Genesis device was developed after study of the Taurus meta-genome. After analysis of the genome, the Federation Department of Scientific Research commissioned the Genesis Project which was supervised by Doctors Carol Marcus and David Marcus. Their experiment involved the creation of a device that was capable of terraforming at a highly accelerated rate allowing the transformation of a lifeless moon or uninhabitable planet. With the support of Starfleet Command, the Regula I outpost was established for the civilian scientists to conduct their research. Later, Starfleet Corps of Engineers was involved in excavating a large cavern on Regula as part of the experiments.
As the project continued through its various phases, Starfleet dispatched the USS Reliant on a mission to find a lifeless uninhabited world in order to test a working version of the Genesis device. During its mission in 2285, the Reliant discovered the planet Ceti Alpha V whereupon the ship was commandeered by the infamous Augment Khan Noonien Singh who learned of the vessels mission. He attempted to get more information on Project Genesis from his nemesis, Admiral James T. Kirk but was thwarted in his plan. He later traveled to the Regula facility where he was looking for the Genesis device and killed many of the station's personnel. Using a mind controlled Pavel Chekov, he learned of the prototype being located in a bunker on Regula and used the transporter to beam the device onto the Reliant. However, Admiral Kirk attempted to stop him and during the skirmish between the two, involving the Reliant and Kirk's own ship, the USS Enterprise, the Genesis device was detonated which killed Khan in the Mutara Nebula. The resulting explosion resulted in the formation of the Genesis Planet due to the energy matrix within the Genesis device. (TOS movie, novelization & comic adaptation: Star Trek II: The Wrath of Khan)
Later in 2285, Klingon Commander Kruge learned of the power of the Genesis device through a sophisticated network of spies with some believing that the Orions were involved in the matter. Kruge attempted to acquire the device in order to use it as a weapon and thus traveled to the Genesis Planet. Once there, he captured Dr. David Marcus and science officer Saavik, using them to blackmail Admiral Kirk in an attempt to get the power of Genesis. During the incident, Kruge was killed during the destruction of the Genesis Planet. (TOS movie, novelization & comic adaptation: Star Trek III: The Search for Spock)
This was, however, not the end of threat caused by Genesis as one of Kruge's crew was secretly an officer within Klingon Security. After Kruge learned of Project Genesis, Karamark clandestinely transmitted the stolen data to the Klingon Security headquarters on Qo'noS. The data along with Kruge's death was what prompted the Klingon High Council to send Ambassador Kamarag to the Federation Council in order to demand the immediate extradition of James T. Kirk. (FASA RPG module: Star Trek IV Sourcebook Update)
In addition to this, the Romulan Star Empire increased their intelligence activities to learn if the technology would threaten the Empire. Several of the more powerful families within the Orion Colonies formally censured the Federation after the restriction of space traffic through the Mutara Sector. Tensions also grew between Starfleet and the scientific community, despite assurances from the Secretary of Starfleet that the Genesis Project had not been intended as a military operation. The response to this criticism was a media blackout and prohibition of non-authorized discussion of the matter. In further response, joint civilian/Starfleet science efforts were dispatched to both the remnants of the Genesis Planet and the cave laboratory within the Regula planetoid. (FASA RPG module: Star Trek IV Sourcebook Update)
In order to take people into account for the unstable protomatter and other elements of the Project, the Genesis Investigation Committee was established. After examining the findings of Admiral Androvar Drake, they concluded that all Starfleet stockpiles of protomatter were accounted for which resulted in the committee deciding that Admiral Drake was not to blame for the incident. They concluded that Doctor David Marcus had acquired the protomatter from outside sources, such as the Klingon Empire. (TOS novel: The Ashes of Eden)
As a result of the incident, the Federation Science Council published the Genesis Report which detailed in depth the circumstances of Project Genesis. This included the finding of the failure of the Genesis device as well as the resultant political fallout amongst the immediate neighbors of the Federation. The Klingon Empire grew increasingly aggressive as they believed the technology to be the Genesis Weapon and brought about increased mining of the Klingon moon of Praxis. Furthermore, in order to prevent the immediate widespread acquisition and deployment of the Genesis device as a weapon throughout the Alpha and Beta Quadrant, the Genesis Nonproliferation Treaty was signed by the numerous powers. (TNG novel: The Genesis Wave, Book 1)
The knowledge of Genesis and its power was not just confined to the primary universe but the mirror universe. In this dark reality where the Federation did not exist, the Terran Empire had learned of Genesis and attempted to use it for their own purposes. They dispatched the crew of the ISS Enterprise under the command of Captain James T. Kirk. Upon breaching the primary universe, he traveled to Vulcan where he sent his version of Spock to mind meld with that primary universe version who had been resurrected by the Genesis technology. Despite their plans, the Terran Empire's attempt at securing the technology was thwarted by their USS Excelsior and the primary universe versions of Kirk and his crew. (TOS comic: "The Mirror Universe Saga")
By circa 2310, Dr. Carol Marcus created a modified Genesis Device, which was to be tested on the planet Pacifica. These tests were halted when a race of sentient beings were discovered hidden in the depths of Pacifica's ocean. (TOS short story: "The Hero of My Own Life")
At some point after 2373, Starfleet supposedly declassified information on the Genesis device in order to train cadets. This facility was raided by a Maquis cell who allied themselves with the rogue House of Kruge. K'Nera was a descendant of Kruge and sought to get the power that his ancestor desired. However, the data was ultimately placed as bait to trap the Maquis. (TNG comic: "The Enemy of My Enemy")
A copy of the Genesis Device was rebuilt and hidden away within a special vault in Starfleet Headquarters. It was forbidden to use it under the advice of Section 31. (STO mission: "Vorgon Conclusions")
The danger of Project Genesis came back to haunt the Federation in 2376 when Doctor Carol Marcus was kidnapped from a classified planet where she had been placed during the time of the Dominion War in order to prevent her work from being used by other powers. She was kidnapped by an race of sentient plants who used their mental illusions to make her create a much more powerful version of the technology. This resulted in the creation of the Genesis Wave, this powerful fields of energy swept through space where it terraformed planets into something more habitable by their species. She was ultimately convinced to end the threat of Genesis by the Klingon Maltz, the only survivor of Kruge's crew at the Genesis Planet. She and Maltz both sacrifice themselves to destroy the space station that would have unleashed a second Genesis Wave into the galaxy. (TNG novels: The Genesis Wave, Book 1, The Genesis Wave, Book 2)
A year later, one of the aliens that had abducted Carol Marcus left a portable Genesis device in the hands of Bajoran Vedek Yorka who believed it to be the Orb of Life. (TNG novel: The Genesis Wave, Book 3)
In 2385, President Ishan Anjar wanted to recreate the Genesis Device and use it against the Tholians. But he was talked out of it by his staff and Admiral Marta Batanides. Cort Enaren told Anjar "reviving the Genesis techology would be a recipe for disaster." (ST - The Fall novel: A Ceremony of Losses)
In another timeline where Spock died in childhood, the Genesis technology was developed by Starfleet which antagonized the Klingon Empire to the point that they declared open war against the Federation. This led to the fall of Earth to Klingon forces and Starfleet considering more militant actions against the Klingons such as the deployment of a Genesis device on Praxis as part of Operation Olympius in order to end the war from a point of strength. (ST novel: The Chimes at Midnight)