Lunar Watchtower
The MBL's first headquarters was an extraterrestrial starship five miles in diameter that was stationed on the Moon. This headquarters was destroyed by Dark Ener-G.
Underground
The second headquarters was on earth and was located underground in Thunder City. This became the MBL's headquarters again after the team's third headquarters was destroyed.
Limbo
The third headquarters was located in the other dimension of Limbo. Rhyme Guardian asked Kid Bucket to use his teleportation powers to create a transporter device that could transport the team into Limbo. The team built the headquarters on earth and transported it into Limbo. Viper destroyed this headquarters with a missile that he transported into the dimension, forcing the MBL to return to their second, underground headquarters.
Seven Senses Headquarters
The fourth headquarters was the former residence of the Seven Senses, located in Thunder City. The MBL moved here after its underground headquarters was destroyed. The Seven Senses Headquarters was destroyed by the Arch-Moderator when he landed on Earth in the form of a gigantic being of power (MBL #6).
U.S. Army base
The fifth headquarters was a disused U.S. Army base that the government donated to the MBL as a temporary headquarters.
Secret Headquarters
The sixth headquarters was somewhere in Thunder City in a secret location originally known only to a few MBL members.
Thunder City Headquarters
The seventh headquarters, built by the Time Trust as a gift to the MBL, was located in Thunder City. An exact replica of this headquarters was built next to it as a decoy. This replica was destroyed by Hate Assbury in "A World Corrupted."
Lunar Headquarters
A second headquarters on the Moon was built as the eighth headquarters after the Thunder City Headquarters was deemed too dangerous to the city.
Lightningburg Headquarters
The ninth and final headquarters was located in Lightningburgh, a suburb of Thunder City.