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In this manner, Descartes proceeds to construct a system of knowledge, discarding perception as unreliable and instead admitting only deduction as a method. In the third and fifth Meditation, he offers an ontological proof of a benevolent God (through both the ontological argument and trademark argument). Because God is benevolent, he can have some faith in the account of reality his senses provide him, for God has provided him with a working mind and sensory system and does not desire to deceive him. From this supposition, however, he finally establishes the possibility of acquiring knowledge about the world based on deduction and perception. In terms of epistemology therefore, he can be said to have contributed such ideas as a rigorous conception of foundationalism and the possibility that reason is the only reliable method of attaining knowledge.

In Descartes' system, knowledge takes the form of ideas, and philosophical investigation is the contemplation of these ideas. This concept would influence subsequent internalist movements as Descartes' epistemology requires that a connection made by conscious awareness will distinguish knowledge from falsity. As a result of his Cartesian doubt, he viewed rational knowledge as being "incapable of being destroyed" and sought to construct an unshakable ground upon which all other knowledge can be based. The first item of unshakable knowledge that Descartes argues for is the aforementioned cogito, or thinking thing.

Descartes also wrote a response to skepticism about the existence of the external world. He argues that sensory perceptions come to him involuntarily, and are not willed by him. They are external to his senses, and according to Descartes, this is evidence of the existence of something outside of his mind, and thus, an external world. Descartes goes on to show that the things in the external world are material by arguing that God would not deceive him as to the ideas that are being transmitted, and that God has given him the "propensity" to believe that such ideas are caused by material things.

Descartes was also known for his work in producing the Cartesian Theory of Fallacies. This can be most easily explored using the statement: "This statement is a lie." While it is most commonly referred to as a paradox, the Cartesian Theory of Fallacies states that at any given time a statement can be both true and false simultaneously because of its contradictory nature. The statement is true in its fallacy. Thus, Descartes developed the Cartesian Theory of Fallacies, which greatly influenced the thinking of the time. Many would-be philosophers were trying to develop inexplicable statements of seeming fact, however, this laid rumors of such a proposition impossible. Many philosophers believe that when Descartes formulated his Theory of Fallacies, he intended to be lying, which in and of itself embodies the theory.[citation needed]