This phrase is a less-common variant of a common metaphor which uses cloudy weather to represent **negative emotion visible in a person's face**. Here are some dictionary sources to demonstrate some other variants of this metaphor:
> If a person's face clouds over, they suddenly look unhappy or worried:
> _At the mention of her dead husband, her face clouded over._
>
> \-- Cambridge Dictionary, **cloud over**, meaning 2
> Used to refer to a state or cause of gloom, suspicion, trouble, or worry.
> _‘the only cloud on the immediate horizon is raising a mortgage’_
>
> A frowning or depressed look.
> _‘a cloud passed over Jessica's face’_
>
> \-- Lexico, **cloud**, meaning 2
> If your eyes or face cloud or if sadness or anger clouds them, your eyes or your face suddenly show sadness or anger.
> _[literary]_
> _Trish's face clouded with disappointment._
> _As he looked at Katherine, great sorrow clouded his eyes._
>
> \-- Collins Dictionary, **cloud**, meaning 6