However, soon the Emperor learns the location of the planet and sends his minions to the planet to capture the Jedi children of Han and Leia, Jacen Solo and Jaina Solo. Joining Kam Solusar and the Brogans, Brand and the others are able to repel the attack by the Dark Side adepts, unfortunately not without cost, as Jem is killed in the battle. Brand and the group are soon forced to retreat and rejoin the Alliance on the remote planet of Nepsis VIII. While there, the Han and Leia and the Jedi Order were soon blessed by the birth of Anakin Solo, who would someday grow up to be a powerful Jedi Knight.

However, the birth of Anakin did not go unnoticed by the Emperor, and as his clone bodies were becoming more and more unstable, Palpatine sought to use Anakin as a new host body transferring his spirit into the infant, free of the complications caused by using clones. Taking the fight to the Emperor, Brand, Luke, Kam Solusar, and Rayf Brogan infiltrate the planet Vjun to deal with Dark Side adepts using Darth Vader's personal stronghold, Bast Castle, as a base. Rejoining the Solos, now on the ancient planet of Onderon hiding in the wilderness, Brand and the Jedi arrive to find that the Emperor had located Leia and the infant Anakin, and was in the process of trying to take over his body.

During the battle with the Emperor, Rayf Brogan was killed, the second casualty in the fight to rebuild the Jedi Order. During the engagement, Palpatine was hit with a fatal blaster bolt and as he faded away left the body and prepared to enter Anakin's. However, Empatojayos intercepted his spirit before it could reach Anakin, and held it within his own body. However, the Dark Side energies that inhabited the Emperor's spirit were too much for Brand's body to handle, as they ate away at him from the inside.

As Brand lay dying, he said goodbye to Luke and the Jedi, taking the Emperor with him. Empatojayos Brand was a Jedi Knight, a beacon of light in a time of darkness. When Empatojayos Brand became one with the Force, he took the Emperor with him, removing his presence from the galaxy once and for all.