Learn Russian: Птица прячется в дупле, потому что в лесу идёт дождь. - The bird is hiding in the hollow because it's raining in the forest.

This highlights the irregular Prepositional (often called Locative) case. A specific group of short masculine nouns take a stressed -у or -ю ending instead of the standard -е when expressing location with the prepositions в or на. Therefore, лес becomes в лесу.

If лес takes the irregular -у ending, why does дупло just become в дупле?

The special stressed -у location ending only applies to a specific set of masculine nouns (like лес, шкаф, сад). Because дупло (tree hollow) is a neuter noun, it simply takes the standard regular Prepositional ending -е.

Why does the verb прячется have -ся at the end?

The base verb прятать means to hide something else (like a squirrel hiding a nut). By adding the reflexive particle -ся to make прятаться, the action reflects back onto the subject, meaning "to hide oneself." Since the bird is hiding itself, we must use the reflexive form here.

Literally, идёт дождь translates to "rain goes." Is this the standard way to say it is raining?

Yes! In Russian, precipitation always uses the verb идти (to go on foot/to move). You will use this exact same structure for other weather events, such as идёт снег (it is snowing).