Without context, it is impossible to say for sure.
"I'll see you in court" (no "the") is a common threat, meaning that you plan to sue the person you are talking to.
"I'll meet you in court" (again, no "the") simply means that you will encounter the person in a courtroom.
On the other hand, "the court," in either sentence, more likely refers to a specific place, like the court of a shopping mall, than to a courtroom.
Context is everything.