#sudden realisation

Crowley knew when Aziraphale was kind to him (even after he had fallen) that he cared deeply for Aziraphale. It took Aziraphale longer and there's multiple points we could place Aziraphale realising how much he cares for Crowley (the books in 1941, possibly their first meeting when Crowley made the stars, possibly when Crowley pretended to kill the goats and Job's children).

Aziraphale and Crowley knew that after they stopped Armageddon that it wasn't going to be the end of seeing the forces of Heaven or Hell. The two of them knew that they could not escape forever, that time does not stand still and that there was no escaping the inevitable.

So after the demons invaded the bookshop and Aziraphale blew up his halo, he knew that Heaven would find some way to pin it on Hell. And Aziraphale was afraid that Hell would blame it on Crowley, and what might happen to his best friend, to the man he loved.

So he went with Metatron to Heaven to protect Crowley. He wanted to go with Crowley but he knew they would never be safe if they just ran off together. The minute either of them performed a miracle it would reveal their location and who knows what might happen.