In 2364, Whalen was serving aboard the Galaxy-class starship USS Enterprise-D when Captain Jean-Luc Picard invited him to participate in a holographic adaptation of The Big Good-Bye. The holodeck program was a Dixon Hill story, set in 1941 San Francisco. Whalen was familiar with The Black Orchid, another novel in which Dixon Hill was also the main character.
Whalen was enthusiastic about participating in The Big Good-Bye with Picard and Lieutenant Commander Data. When the Starfleet officers entered the holodeck, Whalen thought the fictional characters were wonderful and recognized the name of Joe DiMaggio as a baseball player, a sport which he called a "national obsession" in 1941.
During the holodeck program, Captain Picard, playing Dixon Hill, felt guilty that one of his female clients had come to him, telling him that someone was trying to kill her before she was murdered. However, Whalen reminded Picard that his client had always just been a fictional character from a book.
Later, he accompanied Picard and Data to a police station and was fascinated by the recreations of ancient artifacts. He also recognized Felix Leech and revealed that he had read about the character on many occasions. Leech had hired Dixon Hill to find a particular object for him. Since the detective had failed to carry out the request, Felix Leech pulled out a gun and insisted that the object he was looking for would be returned.
As the crew were having trouble with the holodeck, the holodeck safety protocols were disengaged. However, the officers inside the holodeck program had no knowledge of this fact. Whalen, continuing to participate with the holographic characters in the program, promised that Felix Leech would never find the object he was searching for. Moving toward the hologram, Whalen asked for Leech's gun. In response, Felix Leech shot Whalen with his weapon. The historian, shocked that he had been injured by a fictional character, fell to the floor with massive internal bleeding.
Aware that Whalen had to be taken to sickbay, Picard attempted to escape from the holodeck, but the starship's computer would not respond. When the holodeck's exit door was eventually opened, the captain tried to bargain with Felix Leech's boss, Cyrus Redblock. If Redblock allowed the officers in the holodeck to take Whalen's unconscious body to sickbay, Picard agreed to return with the item that Redblock and Leech required. Instead, however, the villainous characters attempted to exit the holodeck themselves, but, as they were holographic in nature, they de-materialized after they left.