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In the game I run the Confusion Bomb has come into play. When we started to dig into some of the mechanics of implementation there were some questions.
Confusion Bomb* (Su): The alchemist's bombs twist the target's perception of friend and foe. A creature that takes a direct hit from a confusion bomb takes damage from the bomb and is under the effect of a confusion spell for 1 round per caster level of the alchemist. Reduce the amount of normal damage dealt by the bomb by 2d6 (so a bomb that would normally deal 6d6+4 points of damage deals 4d6+4 points of damage instead). An alchemist must be at least 8th level before selecting this discovery. [note the FAQ now has a save effect for this]
This spell causes confusion in the targets, making them unable to determine their actions. Roll on the following table at the start of each subject's turn each round to see what it does in that round.
d% Behavior
01–25 Act normally
26–50 Do nothing but babble incoherently
51–75 Deal 1d8 points of damage + Str modifier to self with item in hand
76–100 Attack nearest creature (for this purpose, a familiar counts as part of the subject's self)
A confused character who can't carry out the indicated action does nothing but babble incoherently. Attackers are not at any special advantage when attacking a confused character. Any confused character who is attacked automatically attacks its attackers on its next turn, as long as it is still confused when its turn comes. Note that a confused character will not make attacks of opportunity against any creature that it is not already devoted to attacking (either because of its most recent action or because it has just been attacked).
The key part of the discussion is this: Any confused character who is attacked automatically attacks its attackers on its next turn, as long as it is still confused when its turn comes.
So, when an alchemist throws a Confusion Bomb does:
A) the bomb damage take place first and then the confusion (thus rolling on the confused creatures behavior); or
B) the confusion takes place first, then the bomb damage (thus the 'confused' creature has been attacked and will go after the alchemist rather than rolling on the confused creature's behavior
We had a lively discussion on this, and while I made a ruling for that instance so we didn't bog down the session, I would like input as to what the correct order should be.
For the session we went with option 'B', but looking at it after the fact I'm more of the opinion that it should have been option 'A'.
Thoughts?

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It say "Any confused character who is attacked", not damaged.
The sequence for the bombs is:
- attack
- after a successful attack, you resolve the damage, included the confusion effect, but when resolving the bomb effect you aren't attacking the target, the attack happened before the confusion effect was applied.
It work that way for all the things that cause confusion.
Using a spell on someone is an attack, using a gaze attack on someone is an attack and so on.
All those attack happen before the confusion effect is applied.

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Alchemist, Confusion Bomb: Should this discovery require a saving throw?
Yes. The target of the bomb may attempt at a save against the confusion effect (Will negates, using the bomb's DC).
This will be corrected in the next printing of Ultimate Magic.
—Pathfinder Design Team, 10/29/13
It is one of the Ultimate Magic FAQs.