saḥ — He (the Supreme Personality of Godhead); eva — indeed; hi — certainly; punaḥ — again; sarva-vastuni — in everything, material and spiritual; vastu-svarūpaḥ — the substance; sarva-īśvaraḥ — the controller of everything; sakala-jagat — of the whole universe; kāraṇa — of the causes; kāraṇa-bhūtaḥ — existing as the cause; sarva-pratyak-ātmatvāt — because of being the Supersoul of every living being, or being present in everything, even the atom; sarva-guṇa — of all the effects of the material modes of nature (such as intelligence and the senses); ābhāsa — by the manifestations; upalakṣitaḥ — perceived; ekaḥ — alone; eva — indeed; paryavaśeṣitaḥ — left remaining.
With deliberation, one will see that the Supreme Soul, although manifested in different ways, is actually the basic principle of everything. The total material energy is the cause of the material manifestation, but the material energy is caused by Him. Therefore He is the cause of all causes, the manifester of intelligence and the senses. He is perceived as the Supersoul of everything. Without Him, everything would be dead. You, as that Supersoul, the supreme controller, are the only one remaining.
The words sarva-vastuni vastu-svarūpaḥ indicate that the Supreme Lord is the active principle of everything. As described in the Brahma-saṁhitā (5.35):
yac-chaktir asti jagad-aṇḍa-cayā yad-antaḥ
govindam ādi-puruṣaṁ tam ahaṁ bhajāmi
“I worship the Personality of Godhead, Govinda, who enters the existence of every universe and every atom by one of His plenary portions and thus manifests His infinite energy throughout the material creation.” By His one plenary portion as Paramātmā, antaryāmī, the Lord is all-pervading throughout the unlimited universes. He is the pratyak, or antaryāmī, of all living entities. The Lord says in Bhagavad-gītā (13.3), kṣetra-jñaṁ cāpi māṁ viddhi sarva-kṣetreṣu bhārata: “O scion of Bharata, you should understand that I am also the knower in all bodies.” Because the Lord is the Supersoul, He is the active principle of every living entity and even the atom (aṇḍāntara-stha-paramāṇu-cayāntara-stham). He is the actual reality. According to various stages of intelligence, one realizes the presence of the Supreme in everything through the manifestations of His energy. The entire world is permeated by the three guṇas, and one can understand His presence according to one’s modes of material nature.