Lysandre is a wealthy and influential figure who founded Lysandre Labs, a company pioneering innovations such as the Holo Caster. He publicly portrays himself as a philanthropist committed to forging a better future via technology and research. His past involved extensive global travel aiding those in need, but witnessing beneficiaries grow increasingly demanding and greedy fostered profound disillusionment. This experience cultivated a deep cynicism toward humanity, convincing him of humanity's inherent selfishness and the unsustainable scarcity of global resources. Consequently, he established Team Flare, an organization harboring the concealed objective of reshaping the world by eliminating those he deemed unworthy.

Outwardly, his personality projects calmness and intellectualism, often engaging respectfully with figures like Hoenn Champion Steven Stone. He exhibits genuine scientific curiosity, particularly concerning phenomena like Mega Evolution and ancient energy sources such as the Giant Rock. Beneath this facade, however, lies ruthless pragmatism. He manipulates others to advance his ambitions, notably recruiting the powerful Mega Evolution user Alain by offering resources and purpose. He exploits Alain's desire for strength, assigning tasks under the guise of protecting humanity while secretly progressing his own agenda.

During the events of "Mega Evolution Special III," Lysandre directs operations remotely from his lab. He monitors the emergence of Primal Groudon and Primal Kyogre near Rustboro City, recognizing their connection to the vanished Giant Rock. He contacts Alain and Steven, informing them of the Legendary Pokémon' movements and expressing concern their clash could annihilate the world. He reveals knowledge of Primal Reversion and recounts the ancient legend of Groudon and Kyogre battling over a vast energy source, identifying this source as the Giant Rock.

When the Giant Rock materializes during the Primal Pokémon' battle, Lysandre commands Alain to protect it "for the good of humanity." He observes Alain and Steven intervene with their Mega-Evolved Charizard and Metagross, who struggle against the Primal forces. Following Mega Rayquaza's appearance and subduing of Groudon and Kyogre, Lysandre's forces arrive via submarine. He contacts Steven, announcing the successful capture and containment of the Giant Rock's radiation. He justifies transporting it to Kalos for further study, emphasizing its potential danger. Subsequently, he commends Alain and offers to arrange intense training battles to help him achieve greater strength, all while privately hinting at imminent, world-altering change for Kalos.

Lysandre's ultimate objective, concealed throughout these events, involves harnessing powerful entities like the Giant Rock and Zygarde to enact his vision of a "beautiful world." This vision necessitates the radical reduction of the global population to preserve resources, achievable only through mass destruction targeting both humans and Pokémon. He views Pokémon as magnificent beings tragically exploited by humans, considering their elimination alongside humans a necessary tragedy for a greater good. His actions securing the Giant Rock are a strategic step toward acquiring the power required for this genocidal plan, demonstrating his readiness to exploit crises and manipulate allies like Alain for his hidden, radical goals.