Learn Dutch: Kom je morgen terug? - Are you coming back tomorrow?

It is the separated part of the verb terugkomen (to come back). In Dutch, separable verbs split in a normal present tense sentence. The main action part (kom) goes in the normal verb spot, and the short prefix (terug) gets kicked to the very end of the sentence.

Why is the verb kom instead of komt? I thought the 'you' form gets a 't' at the end.

You are right that the standard statement form is je komt. However, when asking a question, the verb moves in front of the subject. Whenever jij or je comes directly after the verb, the verb drops the 't'. So it becomes kom je instead of komt je.

Why does the time word morgen go before terug?

Because the separated prefix terug claims the absolute final spot in the sentence! The prefix of a split verb must go at the very end of the clause, which forces other details like time words to be placed before it.

I thought morgen meant 'morning'. How do I know it means 'tomorrow' here?

The word morgen can mean both 'morning' and 'tomorrow'. You can usually tell from the context. When it is used as a time word by itself without an article, like in this sentence, it means 'tomorrow'. If you ever want to specifically say 'tomorrow morning', you would use the word morgenochtend.