Shaw's plan was to use the Omen Virus to gather and then delete all of the CIA and NSA's intelligence and upload it into his brain, in an effort to make him the Intersect 3.0.

Daniel Shaw with Intersect Glasses

After Daniel Shaw used the Omen Virus to blackmail Agent Clyde Decker, and escape from jail, he captured Sarah Walker and forced Chuck to retrieve the Macau device from Decker's office, which would enable him to upload all the data stolen by the Omen Virus. This would force the government to deal Shaw and he would have what amounted to complete power over the government as he would be the only one with access to all their intel.

It is unclear whether the Intersect 3.0 grants the user new skills and abilities, though Shaw does say that he has an improved version of the Intersect just before he fought Chuck. Chuck had however uploaded the Omen into the Intersect glasses, so the 3.0 was destroyed as it uploaded, and Shaw's Intersect access was destroyed, the 3.0 never came into being.

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