The clash known as the Battle of Pinnacle Base saw the New Republic in conflict with the resurrected Emperor Palpatine's forces, all for control of the Republic's Pinnacle Base situated on the Pinnacle Moon. Bodo Baas's Master had foreseen some aspects of this very battle.
After Luke Skywalker was brought to Byss, he came to the realization that the Emperor Palpatine, also going by the name of Sith Lord Darth Sidious, was still alive, despite his apparent demise during the Battle of Endor. Thinking it was the optimal strategy to overcome the Emperor given his knack for defying death, Skywalker chose to become his apprentice. Subsequently, Luke's sister, Leia Organa Solo, journeyed to Byss in an attempt to free him. However, she only managed to get herself and her companions captured. Luke, however, was able to assist in their escape and gave them the command codes that controlled the World Devastators that were devastating Mon Calamari, which in turn enabled the New Republic to be victorious in the battle.
However, Luke's attempt to openly defy the Emperor resulted in the Dark Lord of the Sith overpowering him during an intense duel at the Emperor's Citadel located on Byss.
Palpatine made a surprise entrance above Pinnacle Moon aboard the Eclipse, accompanied by two Allegiance-class battlecruisers, another ship and a subservient Luke. The New Republic defenders were caught off guard by Palpatine's sudden appearance, which allowed the Sith Lord to issue demands to the Republic without resistance. He demanded that Leia Organa Solo surrender herself and board his ship, bringing the Tedryn Holocron that she had taken from him. Sidious also said that if the Republic met his demands, he would consider a truce.
After examining the prophecy of Bodo Baas's Master that was revealed to her by Baas's hologram, Leia willingly boarded the Eclipse, where Palpatine was holding her brother, Luke, under his influence. Palpatine attempted to break Organa and bring her unborn child under his influence by provoking Skywalker into attacking her and proving that he was still worthy of following the ways of the dark side of the Force. Leia deflected his attack with her lightsaber and reached out to Luke's remaining good side, which allowed her to free Luke from his mental imprisonment. The Jedi Master then turned against his former master.
Palpatine, now enraged, drew a blue-bladed lightsaber and engaged Luke. The two engaged in a fierce lightsaber duel. The battle was intense and brutal, with both fighters shifting positions, employing a variety of fighting techniques, and exchanging numerous blows. Leia, who was watching the fight, couldn't even see their movements, but she could sense the enormous power of the clash, like massive waves of light and darkness, with the light eventually prevailing. Despite his ferocity and immense power, Sidious was eventually caught off guard and defeated by Luke, who was aided by his sister's Force harmony, resulting in the loss of his left hand.
Despite the loss of his hand, the Sith Lord was far from defeated. He claimed that he knew through the dark side that Luke wanted to overthrow him and take his place as Emperor. Declaring that the Jedi had underestimated his power, and enraged by the loss of his limb, Palpatine summoned a Force storm and began to destroy the New Republic fleet.
Skywalker and Organa Solo used the Force to surround the Emperor with a wave of light side energy, cutting him off from the dark side and, as a result, his power. Palpatine was unable to control the storm, so it spiraled out of control and began to consume the Eclipse. As the ship was torn apart, the Skywalker siblings escaped, taking Palpatine's current form with them. The storm quickly dissipated after destroying the Eclipse.
It is unknown whether the Eclipse's escort fleet retreated or engaged the remaining Republic fleet, or whether they were destroyed when Palpatine lost control of the Force storm. It is likely that they retreated, as the Republic fleet still had a numerical advantage, implying a future New Republic victory.
At the time, it was thought that the Emperor had been killed on his capital ship. Palpatine's spirit, however, lived on, eventually transferring his essence to a new body.
Pinnacle Base, and the entire planet of Da Soocha V, were later destroyed by a single projectile fired from the Reborn Emperor's new superweapon: the Galaxy Gun.
The Battle of Pinnacle Base made its debut in the Dark Empire 6 issue of the Star Wars: Dark Empire comic book series. Authors Tom Veitch conceived and wrote the battle, artist Dave Dorman illustrated it, and colorist Cam Kennedy colored it. Veitch used this as the story's climax, pitting the Sith Lord Emperor Palpatine against the Jedi Knight Luke Skywalker and his sister Leia Organa Solo.
The Dark Empire audio drama eventually featured the Battle of Pinnacle Base, giving the climax a new dimension through the voice acting of John Cygan (Luke Skywalker), Ann Patricio (Princess Leia), and Nick Jameson (Emperor Palpatine). This duel is notable for its role reversal, in which the Jedi wields a red lightsaber and the Sith wields a blue-bladed weapon.
Jedi vs. Sith: The Essential Guide to the Force depicts the confrontation between Luke Skywalker/Leia Organa Solo and Emperor Palpatine's clone, but with some errors. The description states that the meeting occurred on Byss rather than on the Eclipse. Furthermore, Luke wields the green-bladed lightsaber instead of the red one. He switched back to his green crystal after this duel in the Legends canon.