Stevens quickly obtained General Wright’s permission and ordered his warship to steam toward the train depot. Commander Drayton was also on board the Ottawa.

Perhaps foolishly, the Confederate garrison drew the navy’s attention by firing at the gunboat from the train and nearby woods. The Ottawa neared the train and the two engines throttled up to leave the station. Musket shots from the train were answered by the Ottawa’s guns, including the 11-inch Dahlgren. As naval personnel signaled for the train to stop, the warship directed most of the firing at the two steam locomotives trying to disable them. A witness stated that the train’s passengers, "hooted, jeered, and waved handkerchiefs derisively from the car windows."

Chasing the train for about two miles the Ottawa fired shells at it, some of which took effect. One shell killed two men on a flatcar, M. Savage and John M. Thompson. (These two men have been identified as clerks in one source and soldiers in another, but are not listed on the fort’s garrison list.)

While the Ottawa fired at the train, the conductor had cut loose some of the rear cars and put on extra steam and the train managed to escape as it successfully crossed the bridge and passed on to the mainland. The Ottawa was unable to proceed any further because of the bridge. Later, the Confederates burned enough of the railroad bridge to disable it for the rest of the war.

The men of the Ottawa did not know it at the time, but in addition to troops, the train was also carrying the management team of the Florida Railroad. Also on board was David Levy Yulee, a former U.S. Senator from Florida and financer of the Florida Railroad. Yulee was unhurt, but a shell fragment from the gunboat fatally wounded the man sitting next to him and Lt. Cmdr. Stevens unknowingly had come within inches of killing the ex-senator. Yulee is said to have escaped into the bushes and continue fighting the Federal forces throughout the war.