THE FINAL BATTLE
Attack!
You hope you luck out with this. Based on past battles, you're fairly certain four or five hits will take Chandelure out. Any less will give her a chance to retaliate.
Greninja quickly forms the Water Shurikens, just as quickly hurling them at the opposing Chandelure. Each connecting hit takes a huge chunk out of her health, and sure enough, the fourth connects. She drops before the fifth can make contact.
That's Chandelure down and out quickly. You congratulate Greninja on his victory, and await your rival's next Pokemon.
That next Pokemon turns out to be her own original companion: the Grass/Ground Torterra. A Pokemon Greninja is VERY ill-equipped to deal with, as almost any type he takes from his own moves will leave him vulnerable to any Grass or Ground attack.
There are a few good switch-ins you can do here. Lopunny can DEVASTATE Torterra with Ice Punch, as long as she can survive a hit when she switches in. Rotom is currently part-Fire, and his Levitate ability renders him immune to Ground. Scizor's a Bug-type, which is helpful against a Grass-type. Basically, Grass has a lot of weaknesses and you can exploit a lot of them.