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Since necrons for the most part are alot of partially aware robots and some are straight up robots, would a navagator's 3rd eye have any effect on them? I was just reading the battle of the fang and saw that even an essentially soul-less rubic marine could be affected but somehow the bulkhead on the ship doesn't seem to care. Couldn't a navator therefore even kill a land raider's machine spirit if there was some form of self awareness to it?

I believe it only works on things with souls.

Only information I have on this is from the Inquisitor RPG, wit the Navigator archetype. Under the archetypes powers (page 66 of the 2004 Inq. Annaul, or somewhere in the .pdf that's floating around the net) it lists one named 'The Lidless Stare' which, and I quote;

"The Navigator can stare deep into the soul of a single character..."

Because their eye is a direct connection with the Warp, I'd imagine that, as b-man states simply & directly to the point, only something with a soul, a connection to the Warp, can be affected by the third eye.

The Necrons are an entirely soulless race, so I doubt it.