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My captain has a power sword, and combat shield (with bolt pistol).
My librarian has a force spear and bolt pistol.
My chaplain has a croxius and bolt pistol and a jump pack.

Ok, the Master does have lighning claws, but they are standard too.

I have dug up an old chaplain model with a croxius and no right arm, and I am up for a change.

Will it really kill me to give him a storm bolter. I lose an attack, but will the firepower compensate. It doesnt matter too much as this is a miniature I will not be using often but I do want somthing that is still reasonable, not an unplayable lemon.

If you're marching, say with a non-infiltrating command squad or inside a tactical squad, you can shoot the storm bolter as you go, killing a couple models on the way. This presumably makes up for losing an extra attack in closecombat.

I had a vet with a storm bolter that earned his points back and then some nailing genestealers (got the squad below half in the last few turns when they were trying to move away while holding an objective) that saved my butt once. I suppose it would be just as effective on an HQ.

Should be more effective, assuming you took the vet sgt upgrade to get the storm bolter, that is an expensive model. 20pts for the upgrades.

If vet sgts become mandatory, which is the way GW looks like they are heading, then I could do worse than having a storm bolter sgt in a heavy bolter armed tactical or Dev squad.

I like the look of the storm bolter with the shoulder strap hanging down (I think its from the Commander boxset). It should look good on my chaplain. I was thinking of keeping him cheap but he has termie honours as a huge medallion on his chest, so he gets his +1A one way or another.

A storm bolter may well kill as many models as the extra CC attack over the course of the game, but they don't count the same.

A CC kill counts towards winning a combat. Won combats lead to sweeping advances, or chasing down an enemy who can't get away from you.
A shooting kill counts towards one morale check that can generally be rallied from.

The bolt pistol also acts as a multiplier on the return you get from any other CC weapon you buy. A storm bolter isn't horrible, if you're not spending points on any other CC weapon. If you are, I think you're better off with the pistol.

Why not a plasma pistol?

I agree a plasma pistol on a chaplain would complete him.

Having the ability to get an extra wound on a Hive Tyrant or Carnifex before the unit charges in would go along way in keeping that chaplain alive.

I also like the Thunder-hammer/Crozius/Adamantium Mantle combo as it makes him a close combat monster, and a cool looking model.

Now that the Chaos 'dex has shown that a model may use both a pistol/ccw and a two-handed weapon, that restriction on purchasing only 2 weapons (one of which may be two handed) is more clear now. I recently made a new libby (comes with free force weapon, as we all know) and had him purchase a bolt pistol and combi-plasma. He still abides by the purchase limit, has a bolt pistol for the extra CC attack, but now when he pods in he has a combiplasma shot as well. That's what I'd recommend for your chappy, if you want something besides a bog-standard bolt pistol.