Here's an update on our project, I know it's been a while:
1st level: The user encounters environment and explores. The user notices green (healthy) and red (infected) trees in the environment. The user can heal the trees in this level. Once all the trees are healed, the user can proceed to the next level.
2nd level: The user discovers a reason behind the infected trees. The environment is very similar to the first level, but there are larva infecting the trees. The user can "stomp" to kill the larva. Once all the trees are healed and the larva eliminated, the user can proceed to the next level.
3rd level: The user is brought through a neutral zone before they encounter the boss.
Boss: The user has to heal the infected columns. Larva will serve as distractions for the user and will regenerate. The Worm will also lash out at the user.