VATICAN CITY — As the sun set on Rome and on his turbulent eight-year papacy, Pope Benedict XVI, a shy theologian who never seemed entirely at home in the limelight, was whisked by helicopter into retirement on Thursday.

But while Benedict, 85, retires to a life of prayer, study, walks in the garden and piano practice, he leaves in his wake a Vatican hierarchy facing scandals and intrigue that are casting a shadow over the cardinals entrusted with electing his successor in a conclave this month.

Even as he met with the cardinals on his final day as pope, pledging “unconditional reverence and obedience” to his successor and urging the cardinals to “work like an orchestra” harmonizing for the good of the church, the discord was apparent.