At every important event of Merlin's life it rained. It was almost like an additional part of the prophecy (something he'd said once in a very sarcastic mood).
It rained the day he became Arthur's manservant – that one seemingly unimportant moment that shaped the future of all of Albion. Of course no one, and especially not him, had known this at the time.
It had definitely rained the day he killed Nimueh. He'd caused it. Unfortunately for him and Gaius, he hadn't known how to stop it – then.
It chucked it down the day he met Freya – it was due to the rain that Halig had been inside, not out warily eyeing her prison. He'd gotten very wet when they'd made their escape to the 'secret' tunnels of Camelot.
It rained the day Arthur found out about his magic, a much awaited, climatic reveal involving Morgana, an army and a pair of socks. None of which was his fault; despite what Arthur insisted afterwards.
It also rained the day the Arthur promoted him. His first bit of legal magic was stopping said rain. Well attempting to. He had warned Arthur he wasn't any good at weather magic. Some of Camelot's citizens were mentally scarred for life and it undeniably hadn't helped their attitude towards magic.
It rained the day Gwen gave birth to her son. His godson. Only six years old, and already wiser than the prat (without his help obviously).
Merlin and Arthur rode together out onto the battlefield and absently Merlin marked the blood-red sky and gathering storm clouds.
And when Arthur fell on the battlefield, skewered by Mordred's sword; the only thing he could think over the raging chorus of nononono was the fact it was raining.