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I am thinking of using some Mycetic spores. Unfortunately quite a few guys around here run inquisitor+Mystics. But after reading the rules it seems they would only be able to fire at the spore and not the unit inside.

Deamonhunters, page 15, "if a unit of Deamons, a Greaterdeamon or a Deep Striking unit enters play within 4d6" of an Inqusitor with a Mystic Henchmen (roll when each unit enters play), both he and the rest of the retinue may imediately take a 'free' shot at them.

Tyranids, page 54, "Transport Spore: A Mycetic spore always enters play using the Deep Strike rules, even in missions that do not use these rules.

next paragraph first line,"A Mycetic Spore can carry a single unit of up to 20 infantry models or a single monstrous creature within its armoured shell. Once the Myctic Spore has landed, all creature within must immediately deploy."

So the Mycetic Spore Deep Strikes, and after this is finished any unit inside deploys. This would seem to me that the Inqusitor can only target the Mycetic Spore, because the unit inside did not Deep Strike, they deployed after the Mycetic Spore Deep Striked. Correct?

In most every tournament its being ruled the same as a drop pod. For more info check the DH FAQ.

Arguably, you should get to shoot at both, although the same goes for Drop Pods without the FAQ if you ask me.

The reason I say this is the Transport Spore rule states: "A unit that Deep Strikes via a Mycetic Spore cannot..." so the unit coming onto the board in the spore is considered to be deep striking, despite not using standard deep strike rules necessarily.

The deep strike rules have a similar phrase which is to the best of my knowledge "The deep striking unit may move no further other than to disembark from a deep striking transport vehicle" which clearly indicates that when a transport deep strikes both the transport and passengers are considered to be deep striking.

The RAW issue with both of these are that the free shot is "immediate" and so is the deployment from either a spore or a drop pod, since there's no reason for either to take precedence it's impossible to say whether you got to shoot at the pod (and now, the spore as well) before or after the unit deployed, potentially getting the chance to inflict further damage on the unit by destroying it's transport (or in the case of the spore, making it impossible to "place the unit such that every model is within 2" of the Mycetic Spore")

So basically, RAW you should get a free shot at both the Spore and the Unit inside, however the timing of the shot relative to the deployment of the unit within 2" of the Spore is impossible to determine.

RAI, you are probably best of following the Drop Pod FAQ, therefore the unit deploys before the shot occurs, and the shot may be at EITHER the unit OR the spore.

Drunkspleen is dead on correct here.

Yep, I'd say it's the same as a Drop Pod. Which mans the Inq/Mystics can choose either one, Spore or unit.