Wir bleiben zu Hause. Heute regnet es.
Combining with weil:
Wir bleiben zu Hause, weil es heute regnet.
By what rule did the original order of heute-> es become es-> heute? I understand that the verb is at the end after conjunctions.
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German word order is more flexible in main clauses than in subordinate clauses. In a main clause, either the subject es or the adverb heute can come first. It the first example you happened to use the adverb, but it could just as easily have been Es regnet heute. German prefers subject first in a subordinate clause, so the normal phrasing would be ... weil es heute regnet. But as far as I know, it's still a preference rather than a "rule".