Function within the Collective
Due to the Borg acting collectively, certain orders, commands, initiatives, etc. are brought in conflict with each other. The Borg Queen, in her own words, "I bring order to chaos." It can be conjectured that she determines for the Collective Hive Mind what is irrelevant and what is imperative.
The Royal Protocol
There may be one Queen active at any given time, but there is never only one Borg Queen. Kept within the Borg Diamond are thousands of Borg Queen replicas, which are activated whenever the current queen is incapable of functioning efficiently: this is called the Royal Protocol.
The Borg Queen designated as Alpha is the most superior of models used by the Collective, and also the most logical choice for reactivating the Queen when the current becomes dysfunctional. It is for this reason that it was recycled after destruction.
Alpha-1 led the first attempt by the Borg to assimilate Earth in 2367. It was she who gave the order to assimilate Jean-Luc Picard, re-designating him as Locutus. She let him control the cube during the Battle of Wolf 359, while she regenerated. After the battle, she utilized a Borg trans-temporal transporter to take her back in time to the Delta Quadrant, where she remained as Locutus was desimilated and the cube destroyed.
- In 2063, when Jean-Luc Picard asked her how she survived, she cryptically replied that he "thought in such three-dimensional terms". This may be a reference to her escape, since the Borg designate time-travel as manipulation of the fourth-dimension.
Alpha-1 was sent to assimilate Earth in 2373. Though the cube she commanded was destroyed, a sphere escaped into a temporal rift to the year 2063 to assimilate Earth prior to First Contact. This sphere was also destroyed, but not before she and several drones beamed onto the Engine Room of the USS Enterprise-E. Her attempts were thwarted by Jean-Luc Picard, who destroyed Alpha-1.
Alpha-2 was activated when the Federation starship USS Voyager came too close to a nebula that contained the Borg transwarp hub. However, the intervention of Kathryn Janeway from the 25th century complicated things, due to her encounters with the Borg. Alpha-2 assimilated Kathryn Janeway from the 25th century, but in the process infected herself with a neurolytic pathogen, severing the "mental" link shared among the Borg. The damage to the Collective as a whole was quite serious: the entire transwarp hub was destroyed. But Alpha-2's infection did not spread to the rest of the Collective, only those with her in the cube.
The Borg Queen designated as Beta was second-in-activation-protocol after Alpha. She was activated in 2373, after the destruction of Alpha-1, and remained active until 2377, when Alpha-2 was activated. After the destruction of Alpha-2, Beta was reactivated until Alpha-3 could be fully activated.