Kodai only thought he was touching the time ripple. It was all an illusion by Zoroark.
Zorua destroyed Kodai's illusion blocking device when she bit his wrist. Kodai has his pokemon attack Zoroark, which results in Zoroark falling, but not before Kodai is sent packing Team Rocket style, landing in his own stadium. There, he sees video surveillance of his monologue detailing how he caused all the plant life to die in Crown City when he touched the time ripple 20 years ago. Celebi flies into the time ripple, then comes back to heal Zoroark (much like all the Celebis came to heal one of their own in Pokemon 4Ever). Celebi time travels away. Zoroark and Zorua decide to travel with reporters Karl and Rowena.