SharePoint site branding controlled by Permission

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SharePoint

My client needs have multiple agencies with their respective branding(look and feel). Client wants to implement the intranet in such a way that whenever a user logs in SharePoint, they should see their own branding(their own set of colors and pictures) across the SharePoint environment. For eg., user A works for agency A and agency A uses Red, so when user A logs in to the intranet, he should see the whole intranet with Red branding.

So its changing the CSS/masterpage based on the agency to which the user belongs.

Can someone points me to the right direction on how to go about this?

Thanks in advance.