I think the answer is there in Gita:
सर्वभूतानि कौन्तेय प्रकृतिं यान्ति मामिकाम्।
कल्पक्षये पुनस्तानि कल्पादौ विसृजाम्यहम्।।9.7।।
9.7 O son Kunti, all the beings go back at the end of a cycle to My Prakrti. I project them forth again at the beginning of a cycle.(Tr. by Sw. Gambhirananda)
So Sri Vishnu's Prakiti is referred to in the sloka given by you as His companion.But as there is no real distinction between Shakti and Shaktimaan, or Prakiti or Purusha, He remains alone in real sense.
As Sri Ramakrishna says (Kathamrita, 27 October 1882):
When there is no creation, Mahakali (Prakriti) is staying with Mahakaala(Purusha). One can not think of Brahman (or Purusha) independent of Shakti (Prakriti) and of Shakti (Prakriti) wthout Brahman (Purusha).
So Sri Ramakrishna also says the same thing. Purusha and Prakriti merge with one another at the time of pralaya. Sri Ramakrishna used to say that this state is 'beyond dvaita and advaita'.
Prakriti and Purusha are non-separable from each other.This I had discussed in my reply to another question: How are the object and the subject one and the same?