After Lord Buddha had successfully diverted the general mass of people away from the Vedas, Shankaracharya appeared to propagate a clouded form of Buddhism to attract the people back to the Vedas, leaving aside its real import. This was also the desire of the Supreme Personality of Godhead. Shankaracharya is an incarnation of Lord Shiva and he had to imagine some kind of misleading interpretation, and therefore he presented a kind of Vedic literature that is full of atheism. It is stated in the Padma Purana, and quoted in the Chaitanya-caritamrta (Madhya-lila Ch.6:181-182), that Lord Shiva was requested by the Lord to appear as a brahmana to deviate the human race from Him.
“Addressing Lord Shiva, the Supreme Personality of Godhead said, ‘Please make the general populace averse to Me by imagining your own interpretation of the Vedas. Also, cover Me in such a way that people will take more interest in advancing material civilization just to propagate a population bereft of spiritual knowledge.’
“Lord Shiva informed the goddess Durga, the superintendent of the material world, ‘In the age of Kali, I take the form of a brahmana and explain the Vedas through false scriptures in an atheistic way, similar to Buddhist philosophy.'”
The Supreme Personality of Godhead, the Absolute Truth, is not like a material object that can be known by experimental knowledge or sense perception. In the Narada-Pancaratra this fact has been explained by Narayana Himself to Lord Shiva. But Shankaracharya, the incarnation of Shiva, under the order of his master, had to mislead the monists, who favor ultimate extinction. In the conditioned stage of existence, all living entities have four basic defects, of which one is the cheating propensity. Shankaracharya has carried this cheating propensity to the extreme to mislead the monists.
Shankaracharya, by the order of the Supreme Personality of Godhead, compromised between atheism and theism in order to cheat the atheists and bring them to theism, and to do so he gave up the direct method of Vedic knowledge and tried to present a meaning which is indirect. It was with this purpose that he wrote his Sariraka-bhasya commentary on the Vedanta-sutra.
“The Mayavada philosophy,” Lord Shiva informed his wife Parvati, “is impious [asac-chastra]. My dear Parvati, in the form of a brahmana in kali-yuga I teach this imagined Mayavada philosophy. In order to cheat the atheists, I describe the Supreme Personality of Godhead to be without form and without qualities. Similarly, in explaining Vedanta I describe the same Mayavada philosophy in order to mislead the entire population toward atheism by denying the personal form of the Lord.” (Padma Purana)
Although Shankaracharya was attempting to cover the Supreme Lord by his Mayavadi philosophy, he was simply following the order of the Supreme Lord. Therefore, it should be understood that his teachings were a timely necessity but not a permanent fact.