I did a run through myself (Jesus Christ people you post fast), and I got the same as Commando except Greninja only had 5HP. I don't know if either of us were right but I'm just going to go with 5HP, it's easy to make mistakes doing this.
rabidgoodra tried to have Greninja attack both enemies in an earlier post. I didn't count it but I doubt it would have made a difference anyway since by this post Link and Shepard were both on full health. But no worries, you might like what happens now.
Greninja, on falling below 50% health, is angry. His Torrent ability improves his power.
Bonus ability for Greninja: can attack both enemies (still only restores one health).
Greninja, now empowered, lets two water shurikens loose.