Naraku planned on the Infant betraying him from the beginning. Explaining its why it was even created in that form, along with being on the care or Kagura and Kanna. Even the creation of his armor, Moryomaru, was calculated. All just so Naraku could feast on the demons that made it up.
Naraku's miasma is so strong now that it permanently damages Miroku's body and nearly killed him.
The Infant is swallowed back into Naraku, killing him and making Naraku killable again.
The Nulling Stone is sucked into the Wind Tunnel; keeping Naraku from hiding.