The story
X represents an unknown as opposed to the Roman numeral for 10 (initially, Planet X would have been the ninth planet).
Etymology from Wiktionary, CC BY-SA 4.0.
Planet X
Today it means: A hypothetical planet in the Solar system, beyond the currently known outermost planet. (The term was applied to Eris for a short while, when Pluto was still considered the ninth planet.) Full definition →