You have a number of metaphorical possibilities:
The light dawned. From The Bonevski Legacy by F Duerden:
Mo looked confused, "I'm sorry, you're
"Locum, the stand in for
Reverend Meeches. I understand from the bishop may be absent from his
Suddenly the light
dawned for Mo. "So that's why there was no answer at the vicarage
Fell into place. From Encounters: People of Asian Descent in the Americas by R Rustomji-Kerns:
It was the way in which those words were spoken or heard that embodied
the spirit of my father and all his peculiarities. In that moment of
revelation everything fell into place. It finally made sense to me
why my father used to address strangers as "my friend."
Crystalized. From Assassin on Stage: Brutus, Hamlet, and the Death of Lincoln by A Furtwangler
For him, as for Clarke, Booth's performances were a revelation; they
suddenly crystalized the meaning of all poetry and drama and left
a lifelong impression.
The fog cleared. From Don't Look Back: (Lily's Story, Book 2) by C Kersey
I was still by the back door where I had fallen, but Greta had stopped
barking. At first I was groggy an couldn't remember exactly what had
happened, but as the fog cleared from my mind, it all came back to
me in stunning detail.