The Augment Crisis was a series of events that took place in May, 2154 that nearly brought Earth and the Klingon Empire to war. Although the latter blamed Humans for instigating the events, the actual culprits were a band of Augments.
This series began in 2131, when Dr. Arik Soong stole several Augment embryos while chief of staff at Cold Station 12. He escaped to the Trialas System intent on raising a new breed of "superhumans". However, he was caught and imprisoned on Earth which left his "children" to fend for themselves. Eventually, the Augments decided to leave the system. To do so, they hijacked a Klingon Bird-of-Prey and killed the crew. Their bodies were found adrift by the KDF and after analysis, human DNA was found on the victims. This enraged then Chancellor M'Rek, who threatened to retaliate with extreme force. Once Starfleet obtained the evidence, it was found that the DNA was Augment-enhanced.
Capt. Jonathan Archer and the NX-01 Enterprise were tasked with traking down the rogue Augments. Following a suggestion by Dr. Soong, the ship ventured into the Borderlands to look, but ran afoul of the Orions. They attacked the Enterprise and captured nine crewmembers. Those captured were taken to Verex III to be sold into slavery. They were eventually rescued with the help of Soong, who also was able to contact his Augments. They would intervene and chase off the pursuing Orions. The Augments leader, Malik, succeeded in capturing Archer and he traded him for Dr. Soong.
The Bird-of-Prey made for Cold Station 12 to obtain the rest of the Augment embryos. They gained access to the facility by using a captured Denobulan shuttle and quickly took over the station. Meanwhile, the Enterprise headed to the Trialas System looking for clues as to where Soong may have went. There they found an abandoned Augment that gave them parts of Malik's plans. Piecing together the clues, Archer left for C12. They suceeded in beaming down an away team, but they were unable to stop the Augments. They flooded the station with pathogens, stole the rest of the embryos, and left. The Bird-of-Prey had managed to damage the Enterprise and make good its escape.
Soong's plan was to raise the embryos at Klach D'Kel Brakt, inside Klingon territory. Malik, however, wanted to destroy the Enterprise and planned to use a biogenic weapon on the Qu'Vat Colony to spark a war between the humans and the Klingons. When Soong disapproved, Malik mutinied against his "father". Archer was able to bluff his way into Klingon space and after a brief encounter with a D5 cruiser, caught up with the Augments. The Enterprise destroyed the biogenic weapon, but suffered major damage. It was Dr. Soong that gave Archer the Bird-of-Prey's weakness and they took advantage. Rather than surrender, Malik destroyed his crippled ship along with the last of the Augments.
Satisfied with the outcome, the Klingon High Council withdrew its threats of retailation.
(References: Enterprise: "Borderlands", "Cold Station 12", "The Augments")