From The Stargate Omnipedia
An off-world base primarily designed as a fall-back in the event that Stargate Command
falls under siege by an enemy. The Alpha Site is a location neutral to Tok'ra
and rebel Jaffa
forces. The Goa'uld were unaware of the coordinates for the planet that was home to the first Alpha Site, designated P3X-984 by the S.G.C.
When Anubis probed Jonas Quinn's mind, the location of the Alpha Site was compromised. The base was moved to a different (though similar) planet, and was in operation for several months until it came under fire from Anubis's forces. The officer in charge of the facility, Colonel Riley, ordered a self-destruct of the base to protect sensitive information from being taken, as Earth and the Tok'ra were using the Alpha Site to develop a weapon to be used against Anubis's super-soldiers. Many of the Alpha Site's personnel evacuated to the Beta site, the base's off-world back-up.
At last report, over 60 S.G.C. personnel were unaccounted for in the hours following the attack. The second Alpha Site was abandoned, and an investigation failed to uncover who betrayed the base's location to Anubis.
The Serpent's Lair - With the planet under seige by Apophis, the S.G.C. begins sending Earth's greatest minds to the Alpha Site. Daniel gates to the Alpha Site to escape Apophis's exploding ship in Earth's orbit.
Allegiance - The Alpha Site falls under siege to an Ashrak hidden in the midst of the Tau'ri, Tok'ra and rebel Jaffa.
Death Knell - When Anubis's forces attack without warning, Colonel Riley orders as many officers as possible through the second Alpha Site's Stargate before he initiates the self destruct.