A cure to most if not all diseases...(Cures most of the status effects) I can keep you from fire,palsy and even deep freezes...(Refers to status effects) If you use me at just the right time...(Such as dragonites outrage + confusion) You will probably win your fight...(Will help assist in winning the fight)
I summon the tamer of both land and sea, But both will you need to acquire me, Obtained from a wise man, here from the start, For me you'll need both the soul and the heart.
The jewels from ruby and sapphire to summon groudon and kyorge.
Sorry, that's not it :( This is the only attempt so far, so I'll need a few more before I can post a hint.
Wait, ignore this, it's the Jade Stone isn't it?
I summon the tamer of both land and sea, (summons Rayquazza, which subdues Groudon and Kyogre) But both will you need to acquire me, (Need Kyogre and Groudon) Obtained from a wise man, here from the start, (Given by professor Oak...) For me you'll need both the soul and the heart. (...when you show him the Groudon and Kyogre from Soulsilver and Heartgold respectively)
"It doesn't matter who we are. What matters is our plan. You should have respected my authoritah."