This leads Dean to momentarily believe Sam was still possessed by Lucifer. However, it is later revealed that, whilst his body and mind are not in the Cage, his soul is. During the time that Sam was soulless in Season 6, he lacked empathy and behaved like a sociopath.
Sam loses his demon powers, claiming that the force that transported him and Dean onto the plane cleaned him up. He feels tremendous guilt for starting Armageddon and soon learns his acts have revealed a destiny Dean will be the vessel of the Archangel Michael to fight Lucifer.