I take a piece of popcorn each and run it through a mass spectrometer, and then pick the right one.

I have GlaDOS protect the popcorn.

Deadly neurotoxin + GLaDOS... where have I heard that before? :P

Heheeh... well I guess im... STILL ALIVE!

Oh god... xD

While GLaDOS was dealing with the neurotoxin, I stealthily came through and swiped the popcorn. 

I place the popcorn in a deep hole in my back yard then put all the dirt on top of it again.

I see the patch of disturbed soil, so I simply dig it back up. I then bury the popcorn somewhere in the Earth's inner core, before allowing the hole to fill with molten iron and magma.

Thankfully I was already at the earths core.

I now have the popcorn all too myself :P

I keep the popcorn hidden in the earths core: why whould I want to leave it?

I got teleported with it. I grabbed a drill some time later.

I come back and place it in a box in a box...(a million "in a box"s later)... in a box in a titanic safe, programmed by _________.

I easily hack the safe, due to your idiotic encryption method (FCS-16) and simply drill a hole through your boxception.

I then deassemble the popcorn by manipulating the "strings" of the universe, unraveling the popcorn while storing the pattern in my memory.