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• The muffin tray was affected by the same discharge that brought down 815.

• Juliet was baking muffins for the book club.

• The muffins caused a change in spacetime curvature, thus bringing themselves down, and (possibly) flight 815.

• The muffins were poisoned, as part of Juliet's plot to kill Ben, but the universe course corrected and brought down 815 to prevent the planned lunch.

• Juliet was baking the muffins for Mikhail; it has long been known that Russians love muffins. When the muffins were ruined, Mikhail was so cranky he forgot to turn off the island's shields for a passing jet -- 815.

• DHARMA muffin drops (similar to the food drop, not to be confused with Juliet's muffindrop (hereafter referred to as Muffin Drop Zero)) are available via the Flame's computer. Mikhail has been hungrily spamming the muffin drop code; as a result, the thousands of muffins being simultaneously dropped interfered with Flight 815's radar.
  • Henry Gale's ballon crashed because hundreds of muffins dropped on it's smiley face, on top.

• Each week the book club plays a deadly game, where one muffin is poisoned. Muffin Roulette.

• The freighters are coming to the island for the muffins, or possibly a secret recipe, protected by Ben.
  • Also the reason Jack wants to get back so desperatly in Through the Looking Glass.

• The muffins are for Jacob and since Juliet has dropped them, Jacob constantly appears out of nowhere with his eyes widened. He needs the muffins to reincarnate himself.

• They may have been cupcakes.

• The muffins swapped CDs in Juliet's music collection to confuse Juliet knowing the emotional reaction she has when listening to "Downtown." The muffins then commenced stage two of their plan to burn Juliet's hand by misplacing her oven mittens.