I need a pokemon platinum plot explanation

So Cyrus try's to use palkia and dialga to recreate the universe. That pisses off giratina so giratina sucks him into the distortion world

He then goes and tries to defeat giratina, so that he can continue on with his plan uninterferred. So you defeat him before he can beat giratina.

Then Cynthia tells YOU that you have to fight giratina. I get that you have to defeat it to shut down the distortion world so that it can't destroy the real world. But if you defeat giratina, wouldn't that let Cyrus continue with his plan?