Bonsai Defense is a tower defense game based around growing a tree and warding off infections. The player controls the fruit (the towers) on a tree and assigns different roles to them. The goal is to collect a set amount of nectar, produced by flowers. It needs to be managed carefully as nectar dissolves over time and also attracts enemies.

Before starting a game the difficulty level and length can be chosen, as well as one of the three available tree types. The tree is shown in 3D and it is possible to move the camera, rotate and zoom. By clicking on any of the fruits, a role can be assigned. The most important one is the generator that creates juice to empower the other types of fruit. As it travels to other fruit, it will activate other types such as the grower that encourages growth and heals infection, the pruner to cut off branches that have been overrun, the flower to produce nectar, the shooter to engage the enemies, the bomb (requires some time to charge), the webber to trap enemies with juice, and the sleeper which is an idle fruit but more resistant to infection. Roles can always be changed at any moment.

As the infection starts kicking in, various enemies appear such as a hive, a choke bulb, infection, a locust, a behemoth, a flea or a maggot. If they cannot be defeated, it is sometimes need to prune branches permanently. Through vigor produced by growers the tree will also grow into different shapes. There are various other game mechanics to take into consideration, such as generators with excess juice or turning into batteries after an amount of production. When the infection reaches the roots, the tree can turn against the player and a lot of pruning needs to be done to regain control.

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