Code D is a source of mutation for the life in Planet Planta. It was responsible for the hyper-evolution of the planet's plant life. After its deactivation, the plants went back to normal.
Code D was a remnant of a fallen asteroid which crashed into Planet Planta and changed it into the flora planet we see in the beginning of the episode. Upon landing, the heart of the asteroid constructed an organic dome in which it resides, deep in the core. The core is suspended by a complex root system that provides it with nutrients and, in turn, releases alien microbes which carry out daily tasks and cause the plants to rapidly evolve.
Code D resembles a colour shifting crystal surrounded by purple tendrils.