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As well as being an area where crewmembers can relax in their off duty hours, the arboretum's true purpose is part of the science department aboard a starship, where botanists can experiment with various forms of plant life. (TOS episodes: "The Man Trap", "And the Children Shall Lead", "Is There in Truth No Beauty?"; TNG episodes: "Dark Page", "Night Terrors")
In an attempt to bring James T. Kirk out of his shell following the incident at Tycho IV, Gary Mitchell suggested that he take Ensign Lidell on a tour of the USS Constitution's botanical gardens, but Kirk wasn't interested. (TOS - My Brother's Keeper novel: Constitution)
When new personnel were assigned to the USS Enterprise in the 2260s, the arboretum was one of the locations that they were given a tour of by their section leader. When Kell toured the arboretum in the guise of Jon Anderson in 2266, he was amazed that Starfleet would give so much space over to scientific research and plant life, when compared to the layout of Klingon warships. (TOS - Errand of Vengeance novel: The Edge of the Sword)
Julia Crandall retreated to the Enterprise's arboretum in 2267, when she was supposed to be having a romantic dinner with Pavel Chekov. When Chekov eventually found her, Crandall told him that she didn't want to continue on their relationship from where they left it because it was too soon. (TOS comic: "No Compromise Part One")