[SamIAm]

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Maybe i don't pay attention to the show enough.

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Yeah, pretty much.

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It seems like after he woke up and killed the girl(maybe a defensive use of his power)
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and does not have all of his powers.

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He hit her in the head. And then said, straight into the camera "I do not have my powers."

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If i remember correctly i can remember at least 1 time where hiro stopped time and sylar unfroze it, i believe this was the very first encounter between the 2. It seemed like sylar either unfroze time or was able to move around in with Hiro while everyone else was frozen.

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I don't think so. Maybe Hiro was bad at freezing time while he learned to use his powers, but the only person able to break into Hiro's freeze is Peter.