The Viper Lair was the team's headquarters during Season 1.
After Joe Astor had "liberated" the Viper Defender when it was slated to be destroyed, they needed a hideout. Having previously been directed to the account of Michael Payton, at the end of the pilot episode he used the money to buy an abandoned power station on the outskirts of Metro City. As Joe told Julian Wilkes, the power station had been closed for 50 years, and nobody knew about it. Except Frankie Waters, who then suddenly arrived in his Barracuda. Frankie reveals that the power station was also not included in the city survey maps, and that he had hacked into the system and changed the transaction records, so that nobody could find them.
During Season 1, Joe, Julian and Frankie operated the vigilante Viper project out of the Lair. Every time Joe would bring someone to the lair, he would blindfold them, to keep the place a secret.
It's implied that during Season 1, Joe lived at the Lair.