The preposition "в" can be used with both Accusative and Prepositional cases. When it's used with Accusative, its meaning corresponds to the meaning of the English prepositions "into/to": to go to the store - пойти в магазин, to put the pen into a box - положить ручку в коробку; it implies moving into some place. When it's used with Prepositional, it's like using the preposition "in": I'm now in the store looking for some food for dinner - я сейчас в магазине, ищу продукты для ужина; the pen's lying in the box - ручка лежит в коробке. In this case it implies being in some place (within a certain space).