
Yonman |

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It's a specific call out in the rules because many creatures have advantages in that way that would make a character much more powerful. They are "natural" but specific trumps broad and, in this case it seems very straight forward that you just can't do it. It probably also disallows Rend, rake, and pounce as those technically allow extra attacks. They wised up by the time they put out the summoner class. They stopped allowing all the natural attacks for free from being a thing as it was way to strong for a pure martial to get these abilities on top of what they already have.

Yonman |

It's a specific call out in the rules because many creatures have advantages in that way that would make a character much more powerful. They are "natural" but specific trumps broad and, in this case it seems very straight forward that you just can't do it. It probably also disallows Rend, rake, and pounce as those technically allow extra attacks. They wised up by the time they put out the summoner class. They stopped allowing all the natural attacks for free from being a thing as it was way to strong for a pure martial to get these abilities on top of what they already have.
I'm going to assume natural and automatic abilities would be similar to say all "Ooze" Traits. They would be blind, not affected by critical hits, but still susceptible to mind-affecting abilities for instance.

Mysterious Stranger |

The way I see it natural abilities would be those that are based on physical attributes that do not require any training or experience to use. Christopher’s examples are good examples.
A tiger’s claws and bite would be considered natural, its pounce and rake would not because those are things it learns how to do as it grows up. The mind controlling the body is still that of the caster. The caster has not spent time wrestling with other tiger cubs, nor was he taught how to hunt by a tiger.

Azothath |
It says you retain the natural abilities and automatic abilities of the creature. What constitutes "natural" and "automatic"
You don't get more attacks with more limbs, I would assume that is "natural".
in this camp you also have Magic Jar:N5 as it has details in the description. The writers streamlined the older D&D3.5 spell into Possession for the Psychic magic/Occult theme in PF1. There are details in the Possession spell description. I'll mention Skinsend, Shadow Projection, Object Possession (Grtr Obj Possession applies to Constructs) and there are a few others.
I'll point you to Possession - Occult Rules on AoN then scroll down to Core Mechanic.
and Possession - Misc on AoN notes most Outsiders and Incorporeal Undead are not valid targets for having inseparable souls/spirits. You could review Raise Dead spell as this line of spells also talks about this topic.
one thematic point is that creatures need some type of soul or spirit that is separate in order to be possessed. The GM may rule that creatures with a "—" in a mental score are immune to standard Possession spell. This will mainly apply to vermin and some aberrations, constructs, or undead. Grtr Possession may encompass a few more target creatures but I wouldn't bank on it.

yonman17 |
Okay, so basic physical stuff like Polymorph spells are retained, but what about if a creature has Resistance to fire, Spell Resistance, damage reduction, etc?
The Possession spell says you can't activate these abilities, so Spell Resistance takes a standard action to lower, I assume you can't voluntarily lower it?

Azothath |
Okay, so basic physical stuff like Polymorph spells are retained, but what about if a creature has Resistance to fire, Spell Resistance, damage reduction, etc?
The Possession spell says you can't activate these abilities, so Spell Resistance takes a standard action to lower, I assume you can't voluntarily lower it?
Ex, Su, Spell-like abilities(SLA) are different from spells. I would call spells "ongoing magical spells/spell effects/stuff" rather than "physical stuff"(leave that to the mundane and permanent effects). Once an ability activates a SLA, then usually it is treated as a spell effect.
What ability is tied to the body is somewhat gray area (defined but RAW calls out the GM can make exceptions) the GM can tweak on a creature type basis.ADVICE
most casters that do these shenanigans usually have caches of material components and foci stashed about their vicinity and/or give their familiar/pet a pack with magical implements.
It's handy to have several Magic Jar foci being worn by different party members and discuss it BEFOREHAND with your GM. Best for the PC to spend a day and several castings testing what does and does not work and how to identify party members.