Which chakra direction would make the most sense for this story?

For a clear growth arc, I'd go root to crown. It gives the character a grounded starting point, then each stage can build on what she has reclaimed before. Kundalini can enter early as a guide or force she has to learn to work with, rather than appearing only at the end.

That direction is familiar in some contemporary chakra storytelling, but there isn't one universal rule you need to follow. Your story's emotional logic matters more than matching a single map.

Crown to root fits the premise neatly if the central movement is from being displaced or unmoored toward inhabiting a body again. Each downward stage could make the return more tangible, with the root serving as the final claim on physical life.

You don't have to save the main confrontation for the root, either. The spirit could be weakened along the way, while the last stage is about choosing to stay and making the return hold.

The two-pass version gives you the most room for tension. She could descend from crown to root to reconnect with her body, then rise again as she works through the effects of the possession and faces the spirit. The repeated path won't feel redundant if the first trip is about finding a way back and the second is about taking back control.

I'd make the rules explicit through what changes in each realm. That way the direction feels like part of the plot, not just a diagram the character is following.