if you use Rain Dance, and then Thunder, it will always strike without fail.
abilities like Kyogre's (Drizzle) that make it rain, also work with Thunder in combo.

BUT, if rayquaza (Air-Lock) is in battle, this effect is no more!
ALSO, a weather change can disrupt your combo.

using thunder when rain dance is in effect also gives u a 25% chance to break through protect and detect with thunder

it does ? i didn't know that.