In 1 Samuel 20:40, Jonathan is secretly meeting with David to warn him that King Saul, Jonathan's father, intends to kill him. They have a prearranged signal involving Jonathan shooting arrows and sending a boy to retrieve them.

The verse in question, "Jonathan gave his weapons to his boy, and said to him, “Go, carry them to the city,”" signifies the end of their secret meeting and David's cue to leave.

Here's a breakdown:

"Jonathan gave his weapons to his boy": Jonathan is giving his bow and arrows back to the young servant who accompanied him. This is a signal that the 'game' of shooting arrows is over.
"and said to him, “Go, carry them to the city.”": This is the crucial part. Sending the boy back to the city is a prearranged code. David and Jonathan had agreed that if Jonathan told the boy something along the lines of "the arrows are beyond you," it meant danger and David should flee. In this instance the signal is not explicit. However, based on Jonathan's mood at this time, David would be able to tell by his demeanour that the message was to flee, and so this implicit message was enough for David.

Therefore, the verse serves as a covert message for David to understand that King Saul is still intent on killing him, and he must flee for his life.