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The idea of decontamination was to fix and cure humans to their natural DNA structure, as the Sultarians often poisoned them to catch them.

When the had the doctor, they didn't know he was a time lord so they tried to purify his DNA to human and it could have killed him because it would had reconstructed his genes.

I think it's also to get rid of the germs in the Humans which are dangerous to the Silurans which the Doctor needs to keep alive. The Silurian doctor starts to decontaminate the Doctor and Nasreen, thinking they are both human, and although it works on Nasreen, the decontamination starts to kill off 'half of the things that are keeping me alive' in the Doctor. The Doctor tells the Silurian doctor this, and they scan him, see he has two hearts and then they stop the process.

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Q: What was the point of the Doctor's decontamination in Cold Blood?
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