Translation:Marcus nunc in urbem venit.
You can say also "Marcus nunc ad urbem venit."
Word order does matter in Latin. It is inflected.
You can't use in with accusative case. Can you?
You can when you are talking about movement: Here, Marcus is moving himself towards (into) the city.
When in + ablative would be used more to specify where something occurs or is located. Marcus in urbe est -> Marcus is (already) in the city.