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I can't remember....
I really can't recall seeing or being aware of him flying away at all before 'An Invisible Thread', but I am up for seeing it.
According to an episode guide for Sylar, with regard to episode 3...
Mohinder and Eden visit an apartment believed to be Sylar's. When no one answers, Mohinder breaks in. Inside, Eden notes that Sylar has no photographs in the apartment but plenty of books on philosophy, as well as a copy of Chandra Suresh's book. Mohinder takes pictures of the apartment, including a picture of his father's book on a bureau, books on the shelves, and a book in a glass case. He stumbles upon a secret room behind the glass case. Inside is a map similar to one used by the Suresh's, but with many more connections and papers linked to several of them. Eden identifies Nathan Petrelli on one of the links. Mohinder finds another room in the secret area covered by vinyl tarps. Inside, the walls are covered in scrawls, possibly indicating that Sylar's mental state is unbalanced. Writings such as, "Forgive me. I have sinned," are written all over, some apparently in blood.
Meanwhile, a man believed to be Sylar attempts to abduct Molly, who is being held in a safe room in the Los Angeles FBI Headquarters. Matt and Audrey stop him, with Matt protecting Molly and Audrey giving chase. When Audrey pulls her gun, the man somehow forces her backwards against a wall and makes her point her own weapon to her head. When Matt arrives, he shoots at the unknown man. However, when Matt turns to check on Audrey, the man stands back up and the bullets Matt had fired at him seem to fall to the ground. As Matt and Audrey look back, the man disappears.
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