Dirty cop Vin Makazian told Tony he had a rat in his organization and pointed the finger at Sal. Tony assigned Paulie Gualtieri to investigate, and to kill Sal, but only if he explicitly saw proof.
At a bath house with Paulie, Sal refused to undress, blaming high blood pressure and alleging it would be bad for his back, but implicitly suggesting (to the viewer) it could really be because he was wearing a wire. This raised the crew's suspicions further, especially after Sal then disappeared. Paulie took over his collections, and the crew killed Altieri, taking the heat off Sal, as the crew figured the rat was flushed. Sal resurfaced at Tony's home in 2000, claiming to have been in Puerto Rico receiving treatment for his bad back from an acupuncturist. He started lying to Agent Lipari, showing reluctance to divulge details. Acquaintance Jimmy Bones, who is later murdered at his home for fear of revelation, spots him with Agent Lipari.
Sal and his wife Angie begin having marital issues when he returns.
Angie discusses leaving him with Carmela, who dissuades her, so she settles for sleeping in separate bedrooms. When Tony became acting boss, he made Silvio his consigliere, and Paulie a capo, with new addition Furio Giunta on equal footing with Sal despite Sal's years of service.