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DRAGON
Hit Die: d12.
Attack: Good.
Fortitude: Good.
Reflex: Good.
Will: Good.
Skill Points: 6.
Proficiencies: None.
Class Skills: Concentration, Diplomacy, Escape Artist, Intimidate, Knowledge, Listen, Search, Sense Motive, Spot, Use Magic Device, any three others.
Immortality: The dragon doesn't age.
Immunities: The dragon gains immunity to paralysis, sleep, and one energy type (or another kind of effect roughly as common).
Bite: The dragon has a bite primary weapon, with a base damage of 1d8 for a Medium dragon, plus 3/2 its Strength modifier.
Breath Weapon (Su): The dragon can emit a deadly breath weapon of the energy type to which it has immunity. As appropriate, it will either come out as a cone with short range, or a line which is twice that long and has a width of 5 feet plus 5 feet per ten class levels. The breath weapon deals 2d6 damage per character level, with a Constitution-based Reflex save for half. Once used, this breath weapon cannot be used again for 1d4+1 rounds.
Claws: At 2nd level, the dragon gains two claw secondary attacks, with a base damage of 1d6 for a Medium dragon, plus its Strength modifier.
Draconic Scales (Ex): At 2nd level, the dragon gains an enhancement bonus to natural armor equal to half its class level.
Draconic Strength (Ex): At 2nd level, the dragon gains a +2 enhancement bonus to Strength. This bonus increases by +2 every four levels after 2nd.
Draconic Toughness (Ex): At 3rd level, the dragon gains a +2 enhancement bonus to Constitution. This bonus increases by +2 every eight levels after 3rd. Also, the dragon gains an extra 3 hit points per class level.
Flight (Ex): From 3rd level on, the dragon's wings grow enough to allow flight, giving it a fly speed equal to its land speed, with poor maneuverability for a Medium to Huge dragon; Small or smaller dragons have average maneuverability, and Gargantuan or larger dragons have clumsy maneuverability.
Bonus Feat: At 4th level and every five levels thereafter, the dragon gains a monstrous feat for which it meets the prerequisites.
Size Increase: At 5th level and every five levels thereafter, the dragon grows a size category, except its ability scores remain unchanged.
Sphere: At 6th level, the dragon gains basic access to a sphere (or upgrades access already had). Every six levels thereafter, the access to that sphere improves; if it is already expert, the dragon gains a monstrous feat instead.
Draconic Senses (Ex): From 7th level on, the dragon gains 60' darkvision and sees twice again as far in low-light conditions. Both benefits are cumulative with existing darkvision or low-light vision.
Strengthened Wings: From 7th level on, a landed dragon can make secondary natural attacks with both of its wings, with a base damage of 1d6 for a Medium dragon, plus the dragon's Strength modifier. Also, the dragon's fly speed doubles. Every four levels after 7th, the fly speed multiplier increases by 1.
Damage Reduction (Su): At 8th level, the dragon gains damage reduction equal to its class level, pierced by magic weapons.
Tail: At 8th level, the dragon gains a tail secondary weapon, with a base damage of 1d8 for a Medium dragon, plus 3/2 the dragon's Strength modifier. Also, the dragon can, as a standard action, sweep its tail over a half-circle of radius equal to its reach; all creatures three or more size categories smaller than the dragon are hit and take normal tail damage, with a Constitution-based Reflex save for half; also, they are each subject to either a bull rush or a trip attack.
Blindsense (Ex): At 11th level, the dragon gains 60' blindsense.
Spell Resistance: At 11th level, the dragon gains spell resistance equal to 5 + its character level.
Frightful Presence (Ex): A dragon of at least 13th level can unsettle foes with its mere presence. The ability takes effect automatically whenever the dragon attacks or flies overhead. Creatures within a radius of 15 feet per class level are subject to the effect if they have fewer HD than the dragon. A potentially affected creature that succeeds on a Charisma-based Will save remains immune to that dragon’s frightful presence for 24 hours. On a failure, creatures become shaken for 4d6 rounds (frightened if have 6 fewer HD, or panicked if they have 11 fewer HD). This ability doesn't stack with itself (even if used by more than one creature). Dragons ignore the frightful presence of other dragons.
Blindsight (Ex): At 16th level, the dragon gains 60' blindsight.
Crush (Ex): A dragon of at least 17th level can land on opponents as a standard action, using its whole body to crush them. A crush attack affects as many creatures as can fit under the dragon’s body, as long as they are all three or more size categories smaller than the dragon. Creatures in the affected area must succeed on a Constitution-based Reflex save or be pinned, automatically taking damage equal to a tail attack, without another save. If the dragon chooses to maintain the pin, treat it as a normal grapple attack. Pinned opponents take damage from the crush each round if they don’t escape. For all effects of the crush attack other than area covered, treat the dragon as one size category larger than normal.
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I'm sure crush needs more cowbell, and suspect the breath does as well. Also, I expect the stuff that differentiated dragon races to come from races and monstrous feats.