The "S.S. Bonnie Raitt" is Roger's spaceship that he crash landed near Roswell, New Mexico in 1948. Roger believed he was sent to decide if humanity was worth saving but later finds out that he was used as a crash test dummy by his own people in "Weiner of Our Discontent".
After passing himself off as human for a number of years, Roger was eventually caught and held until rescued from Area 51 by Stan Smith. During the interval, Roger had stored the remains of his ship in various storage units including U-Rent Storage and Thrifty Storage.
When the Rapture arrives in "Rapture's Delight", he finds out that Francine had given away important spare parts to Goodwill, thinking they were t-shirts. Near the end of the Tribulations, Stan and Jesus Christ find Roger frantically working to rebuild his spaceship with the help of Qui-Lo inside of a former Anthropologie store. Although flight-worthy, Roger lacks a power source of precious metals and gems until Jesus produces The Golden Turd that Roger had crapped out in "Homeland Insecurity". In exchange for the turd, he agrees to fly Stan and Jesus to the United Nations Building to face the Anti-Christ but Roger crashes the ship and it refuses start again. This ship has a notably different design than seen in the storage units.
When Roger agrees to return to his home planet after Jeff Fischer learns he is an alien in "Naked to the Limit, One More Time", he proceeds to the Thrifty Storage where he notes that it is broken down, filthy, and has a cockpit full of mouse turds. He places the call and arranges to be picked up at the Chimdale mountains but shoves Jeff into the mother ship's tractor beam, sending him into space instead.