Instead of going in hot pursuit of the Straw Hats, Jonathan decides to set a trap for them in Dock 88, where the Going Merry is moored, as he knows this is where they will surely go. He tasks Lieutenant Commander Drake to set up the ambush in Dock 88 and since it will take Drake some time to arrive at said dock, he sends Unit 55 to slow the Straw Hats down to stall for time. He stations them at the bridge which is the only way to get to the ship.

(Source: One Piece Wiki)