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Imotekh the Stormlord unique "Lord of the Storm" power says:
"Once per battle, in your Shooting phase, this model can call the storm. If it does, select one enemy model within 48" of and visible to it (you can only select a CHARACTER model with a Wounds characteristic of 9 or less if it is the closest enemy model to Imotekh). Roll one D6 for each other enemy unit within 6" of that model: on a 4+, that unit suffers D3 mortal wounds. Then roll one D6: on a 4+, that model suffers 3 mortal wounds.

The power description says that you can select an enemy model, not a unit. Let's say that my enemy uses 10 man squad of Chaos Legionaries and gives the Champion "Black Mace" relic. Usually you would need to kill 9 Legionaries before you could take out that Champion but can you just straight up kill the Champion without caring about other Legionaries by using Imotekh power?

They seem to have made the assumption that you will use it on single model units like tanks or whatever. Usually they would have the last line say 'that model's unit suffers 3 mortal wounds', which allows the controller to assign them elsewhere. In my opinion they have screwed up, but they haven't bothered to FAQ it in over two years, so who knows. RAW, it does appear to allow him to snipe individual characters out of a unit like you say.

The necron codex was written years ago when you werent able to give unit champions a relic, or a special item. I guess no one noticed until now, because imotekh is not played in todays necron lists.

RAW, you can snipe the champion.

 p5freak wrote:
The necron codex was written years ago when you werent able to give unit champions a relic, or a special item. I guess no one noticed until now, because imotekh is not played in todays necron lists.

RAW, you can snipe the champion.

From this it follows that if the targeted model dies, the mortal wounds are lost, because if they affect other models in the unit, it's no longer "that model suffers 3 mortal wounds", but rather "that models unit suffers 3 mortal wounds".

Seems that way. The interaction is obviously unintended, which results in weird deviations from normal gameplay.