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Near the end of season eight, Penny is infected by a virus and subsequently saved through the intervention of the spirit of the Staff of Creation. The only thing is, I didn't quite understand what Ruby and the others told the spirit to do. They told him to create a new version of Penny, but there was something in there about how the spirit couldn't destroy her soul and thus this little nuance would force him to save her. And I think Ruby said something about copying the virus as well. It was a bit confusing. I'm not entirely sure whether Penny's soul stayed in her old body and the virus was put in the new one, or if Penny's soul went into her new body and the virus was put in the new one.

What happened?

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As these things sometimes go, the answer came to me after some thought. It took a while for some of the details to sink in. I believe I can explain what happened with some clarity now.

First, the order to the spirit of the Staff of Creation was to create a new version of Penny, exactly the same at the current one, with the virus still in it, out of the same parts as the current one. This would cause the current Penny to be destroyed. However, here comes the loophole: the Staff of Creation is not allowed to destroy (or create) life. Penny has a soul, as evidenced by her use of aura, therefore he cannot follow this order. His only choice is to give Penny a flesh-and-blood body.

This explanation meshes well with some details that initially confused me. For instance, Penny starts hugging everyone immediately after and marvels at how warm hugs are. And in the final episode of the season, she has blood.

The wiki seems to confirm my suspicions:

In "Creation", she was transformed into a Human by Ambrosius when he created an exact replica of her using her robotic parts.

Disclaimer: I did this answer from memory, rather than consorting the episodes again. But I think my memory is accurate in this case. Hopefully. Feel free to correct me if I got any of the details wrong.

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