While the Cold War kept the galaxy in suspense, a male Falleen claimed to be the infamous Lost Prince who was kidnapped 20 years ago. The royal family of Falleen consequently hired someone to verify the claims. The Falleen was eventually exposed as an imposter and admitted under arrest, that he was the son of one of the prince's original kidnappers as well as that true prince died years earlier.
In the years following the Battle of Naboo, Falleen experienced a boom in the construction of factories and manufacturing facilities, as corporations found it was less costly to maintain such facilities on remote planets.
During the Clone Wars, the planet was represented in the Galactic Senate by Zurros, who served as a double agent for Count Dooku until Falleen openly joined the Confederacy, though it took a land invasion and coercion of the Falleen King to complete it.
Later, during the early years of the New Order, Darth Vader established a bacteriological research outpost on the planet. When a highly-destructive flesh-eating bacterium got loose in 7 BBY, Vader ordered his ships in orbit to raze the laboratory and the city surrounding it in order to save the rest of the planet. Vader wiped out the bacterium, along with an entire city and over two hundred thousand Falleen, including the royal House Sizhran. However, biological and chemical research for military purposes continued on the planet in other locations.
Decades later, Falleen, which never joined the New Republic, fell to the Yuuzhan Vong, shortly after the destruction of the Fondor shipyards and Hosk Station. After the war's end, the planet remained unaligned and isolated.
In 138 ABY the One Sith sent the Darklight, an Imperious-class Star Destroyer to bombard the planet into submission. However the plan was foiled by the Mynock crew and Rogue Squadron who destroyed the cruiser.