Ten thousand years ago, Zarkon brought Honerva into the trans-reality rift on Daibazaal in an attempt to save her from her ailing health. She was already pregnant with Lotor. After presumably dying from the over-exposure to Quintessence, Zarkon and Honerva reawakened in a corrupted state from their ordeal and began waging war across Daibazaal's solar system in pursuit of Voltron and establishing the tyrannical Galra Empire.
The experience in the rift did not kill the unborn Lotor; instead, it infused him with copious amounts of Quintessence, and he continued to grow in Honerva's womb. When she was ready to give birth, complications threatened Lotor's life, but technicians managed to save him at Zarkon's request. Honerva eventually took on the identity of Haggar and forgot that Lotor was her son - along with her entire life as Honerva. The prince's Altean heritage was seen as a weakness by many, but Lotor embraced it as a strength. His unique gestation allowed Lotor to age, at least physically, much slower than other Galra.
When old enough, Lotor was assigned to govern a planet and oversee its civilization's mining of Quintessence for the Galra Empire. Instead of brutally subjugating them and mining Quintessence to the detriment of the planet, he befriended the civilization, enjoyed their culture, and only mined as much Quintessence as could be replenished. Enraged, Zarkon ordered him to destroy the planet, but Lotor refused, so Zarkon exiled his son and destroyed the planet and its entire civilization himself. Lotor lamented being powerless against his father's tyranny and spent the next several centuries searching for clues about his Altean heritage; he gained substantial knowledge about the universe, including the Alteans, Voltron, and Oriande.
Lotor eventually created a colony constructed as a make-shift Altea on a planet in the Quantum Abyss and tracked down surviving Alteans in hiding who were not present on Altea when it was destroyed, as many had been on trading expeditions at the time, and convinced them to live in his colony where the distorted space of the Quantum Abyss would keep them hidden from the Galra Empire. The Alteans in the colony flourished and came to worship Lotor as their savior.
As time passed, Lotor claimed he had created a second colony only certain Alteans were fit to travel to. It was considered the highest honor to be selected, but communication between colonies was banned so no one would find either's location. In truth, Lotor was selecting Alteans with high Quintessence to be harvested on the planet's moon in order to unlock the secrets of Quintessence and create abnormally-concentrated Quintessence to power his own ships. The process killed thousands over many generations. Bandor was selected and found out the truth, managing to escape and warn his sister, Romelle, before dying. Lotor spotted her as she fled the scene of her brother's death, but let her go. Romelle told no one the truth, thinking she would not be believed.
Lotor eventually took in Acxa, Ezor, Narti, and Zethrid - all part-Galran women - as his top generals; he became famous for allowing planets he conquered to rule themselves and for fighting alongside his armies like a lowly private - things regarded with disgust by the military elite of the Empire. At some point, he discovered the second Trans-Reality Comet originally located by King Alfor, but was unable to retrieve it from the spacecraft stuck in a trans-reality rift, as all his pilots and spacecraft did not survive the attempt.
The prince does not return to the Galra Empire until Zarkon's obsession with the Black Lion leads to the emperor's defeat at the hands of the Voltron team and their allies, putting Zarkon in a comatose state under the care of Haggar. The exiled prince is summoned by the witch to lead in his father's stead.
The Galra Empire is brimming with treachery by the time Lotor arrives. Distrustful of Haggar for the witch's refusal to let anyone speak or see Zarkon, Throk plans to usurp the throne with backing from the generals in his sector and asks for more assistance from another Galra commander at the Empire's gladiator arena, where the audience is filled with military personnel gathered to watch a small masked warrior battle a massive beast.
Unbenkownst to Throk, Ezor and the other generals of Lotor's royal guard sit hidden in the audience around him, listening and relaying the conversation to Lotor himself - the very warrior Throk is watching fight. When the beast is defeated, Lotor removes his helmet to reveal his identity and publicly calls out Throk's treachery to the audience, offering to accept the commander's challenge for the throne through honorable combat. With his plans exposed, the pressure of the audience upon him, and the royal generals blocking his escape, Throk agrees to the duel.
After a ferocious fight, Lotor stands the victor and Throk waits to be slain, but the prince spares his life, giving a rousing speech to the audience about inspiring loyalty in their conquered foes instead of fear. His speech wins over the support of the Empire's military and that of Throk, who pledges his loyalty. Soon after, Lotor meets with his generals and orders them to transfer Throk to the far reaches of the Empire to rot.
Lotor's next move is to travel to planet Puig that has just been freed from the Galra Empire's control by Team Voltron and left unguarded. His generals are able to overpower the defenseless people without casualties, and Lotor personally offers their leader a chance to join the "new" Galra Empire, claiming they will never need Voltron's so-called protection again. Apparently refused, he leaves Puig to study the movements of the Voltron Lions on his Royal Warship, intrigued that there have been no recent sightings of the Black Lion, speculating it means that Voltron is unable to be formed. He sends Narti to Puig, who uses her mind-control powers to control the Puigan leader, sending a false call for help to Team Voltron to lure them to his location.
The prince is not aware that Keith has suddenly become the new Paladin of the Black Lion because of Shiro's mysterious disappearance. When the Voltron team arrives, Keith, Hunk, and Pidge are the only Paladins able to leave the Castle of Lions in a Lion, as the Blue Lion refuses to respond to Lance. Lotor greets the three Paladins outside of Puig from his Royal Warship, declaring himself the son of Zarkon and Emperor Pro Tem of the Galra Empire.
His fleet of fighter jets proves a worthy match for the three Paladins to handle, but Lotor is calmly nonchalant that the Black Lion is functioning and wonders about the two missing Lions. With more fighters launched to force the Paladins into a desperate situation, Lance is soon chosen by the Red Lion for his matured heart and acceptance of Keith as the new leader; he enters the battle to assist the other three Paladins, but with little handling of his new Lion.
The team's disarrayed display means Lotor notices that the Black Lion's pilot is not in full control. After the Royal Warship's ion cannon deliberately blasts the Black Lion and the Castle of Lions, Lotor's probing bears fruit: Allura arrives in the Blue Lion, newly chosen as its Paladin. With the truth revealed that all Voltron Lions are functioning, Lotor believes he has witnessed enough and retreats with his fleet instead of continuing the fight.
Unbeknownst to him, Keith has placed a tracker on the Royal Warship and orders the team to pursue Lotor to end his reign immediately. Once the Lions are detected, Lotor meets them in battle in his own fighter jet, easily using its agility and the Paladins' own unorganized state against them. It becomes clear that the Paladins are not the same ones who defeated Zarkon and that they cannot form Voltron, so Lotor orders his generals to recalibrate his fighter jet and to hover above Thayserix as he leads the Paladins into the dangerous planet's atmosphere, plotting to capture the Lions one by one.
Keith's aggressive and hyper-focused nature causes the team to fall into Lotor's trap. Thayserix wreaks havoc on the Lions' navigation and communication systems while Lotor's fighter jet remains unaffected, and the planet's nitrate gases react to the Lions' weapons, causing a dangerous explosion. Lotor successfully separates the team and pursues Allura, who is struggling to connect with the Blue Lion. However, Allura manages to bond with the Lion and use its Sonic Boom Cannon to navigate Thayserix, outwitting Lotor and freezing his fighter jet's left wing with the Lion's Freeze Ray, forcing him to retreat to his warship. Allura locates the other Paladins and the new team properly bonds to form Voltron.
His plan failed, other Galra commanders appear to assist Lotor in handling Voltron, but Lotor leaves once the commanders' warships are destroyed. Acxa questions if the new Paladins being able to form Voltron will be a problem, but Lotor merely considers it an opportunity.
Team Voltron soon detects a distress signal used by King Alfor's deep space vessels and finds Commodore Trayling's ship trapped in a trans-reality rift in the middle of space. The signal has been set by Lotor, as he believed only Voltron could successfully pass through the rift because it was made from a similar comet. He decides that whatever the outcome, it is a win either way: if Voltron disappears into the Alternate Reality, then he loses an adversary, and if Voltron returns with the comet, he will simply take it from them. Upon their return, the latter proves true: Lotor attacks Voltron immediately and sends his generals to retrieve the comet before the Paladins can retaliate. Although they cannot hear it, he thanks the Paladins for answering his distress signal.