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- The monster killed Seth Norris because he was not Frank Lapidus. Frank was supposed to come to the Island, not Norris, so the monster had to correct this.
- We're aware the Man in Black could take the form of the deceased. The Man in Black killed Seth in order to take and use his form to perhaps mingle with the survivors. Under the pretense of being Seth, this would have no doubt been a good disguise to operate under and manipulate with towards his goal of leaving the Island. However this did not come to fruition as Jack, Kate and Charlie witnessed Seth's death, so this plan had now become redundant. This may also serve to explain why the Man in Black chased the trio in his monster form afterwards, to eliminate the witnesses so he could carry out the plan. Ultimately he was unsuccessful and with his plan ruined, the Man in Black set into motion further plans we see later in the show.
- Seth was killed for bringing more people to the Island. MIB was unhappy about people arriving in The Incident, Parts 1 & 2 and MIB killed Seth in a rage.
- The monster killed him because he was the only survivor of the crash who knew, roughly, where the Island was, and the monster needed to protect it.
- The monster killed him mistakenly, thinking he was Frank Lapidus.
- Maybe his body was never found and appeared as a manifestation/ghost.
- It wanted to "flex its muscles" so to speak.