The Borg Elimination Incident occurred in mid-2384. (Star Trek: Unity)
Background[]
After several attempts by the Borg to invade the Federation over the previous few years, the Federation fought back and developed a nano-virus which would eliminate all collective connections by destroying the vinculum, the connection device in the center of each Borg vessel. This would disrupt the drones' individual connections and leave each drone dead. In addition, the explosion caused by the vinculum's destruction would blow up each vessel.
Opportunity[]
In 2384, the Borg attacked the Alliance through a newly built Borg transwarp hub inside a small nebula. Starfleet decided that this would be the perfect opportunity to destroy all Borg because the hub's connections would allow the nano-virus to be sent through each transwarp aperture to every Borg ship and station.
The Alliance ships attacked the Borg, while a special task force led by captains Jean-Luc Picard, Lewis and Cortez sent the nano-virus through the transwarp apertures and to all the Borg fighting Alliance forces.
The effect was devastating. Within hours, very few Borg were left. Probes sent to Unimatrix One found crippled starbases, debris and general chaos. The Alliance declared the operation a success and the Borg were thought to be wiped out. The Alliance then captured the transwarp hub.
Aftermath[]
The Borg emperor and the Rakelli[]
However, the Borg were not totally neutralized. A single Borg cube which had been out of range of the virus managed to survive with its Collective intact. It hid in the Azure Nebula and repaired. During this time, a Rakelli freighter crossed its path. (See: Rakelli.) However, it was not until the Battle of Gateway a year later that the Borg were considered a galactic power again.
The Borg queen's survival[]
Unknown to Starfleet and the Borg "Emperor", the Borg Queen survived the incident by enveloping her ship (and a small number of others nearby) in a Emergency Temporal Shift bubble which transported them to 2387.