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Hekaton land fortress with ion beamers fires up a unit, and it uses the Ion storm strategem. There is an intervening unit that also gets some of joy as the beamers are, well, beams.

Which means for every hit on the original target, the intervening unit gets a wound rolled against it as well. So does it also get MWs on 6's to wound it?

The stratagem says: "...Until the end of the phase, each time a model in that unit makes an attack with an ion weapon, an unmodified wound roll of 6 inflicts 1 mortal wound on the target in addition..."

Errata says: "Q: When a beam weapon causes a wound roll to be made against
an intervening unit, does that unit count as having been hit by an
attack for any other rules purposes?
A: No."

So I guess the question is does the intervening unit also count as a target? It didn't get an attack roll rolled against it so no, but it does get a wound roll rolled against it, so kinda...yes?

Ion storm stratagem does 1 MW to the target...

Only the until you selected gets the MW's

intervening units are not a target as per the rules for 40K.

 DeathReaper wrote:
Ion storm stratagem does 1 MW to the target...

Only the until you selected gets the MW's

intervening units are not a target as per the rules for 40K.

Agreed. The FAQ also reinforces this. You only have 1 target unit, even though others may be affected in some way.