Summary
Giovanni is a dark and serious villain in the Pokemon anime, willing to threaten physical violence against both humans and Pokemon. Giovanni uses fear tactics to control Mewtwo and manipulate Meloetta, showing his ability to be a terrifying enemy. Giovanni's dark impulses manifested when he got his hands on the Reveal Glass, causing him to plot the destruction of the Unova region.
The Pokémon anime isn't exactly known for its scary villains, but there's one villain who regularly gets so depraved and dirty that it's scary to deal with. Of course, that villain is none other than Team Rocket's big boss, Giovanni himself.
Many of Giovanni's appearances in the anime are through Meowth's fantasies about how the trio would be rewarded for successfully completing their goals, giving the impression of Giovanni as a goofy, happy-go-lucky guy. seems, but that couldn't be further from the truth. Although Giovanni rarely sees direct action in the Pokémon anime, those times he does he proves himself worthy of the title of leader of one of the most preeminent evil teams in the series.
Giovanni proves that he's not afraid of getting his hands dirty, and he takes the idea much more seriously than Jessie, James, and Meowth.
Giovanni threatened physical violence on several occasions
In the special episode titled “Mewtwo Returns,” Mewtwo actually returns to the story, settling in a place called Quena Mountain with his clones from the first Pokémon movie. Of course, Mewtwo was originally created by Team Rocket and used by Giovanni as a super weapon, wiping the floor with gym challengers like Gary even while wearing a power-inhibiting armor, before escaping from Giovanni's control. In the special, Giovanni tracks down Mewtwo and tries to motivate the Legendary Pokémon to cooperate with him again.
He does so by threatening to experiment on other clones until they “leave this world,” one of the few instances of humans threatening to kill Pokémon in the entire series.. While Giovanni is ultimately defeated and has his memory erased by Mewtwo, the threat and attack on Mewtwo's peaceful hideout shows just how dangerous Giovanni truly is when he acts. Nor was this the only such occasion; Later, in Pokémon Black & White, Giovanni orchestrates a plan to protect the mythical Pokémon Meloetta and gain control of the Reveal Glass, a special artifact.
Similarly, Giovanni also attempted to coerce Meloetta, this time threatening to kill Ash and Pikachu by crushing them in a shrinking force field, leaving Meloetta no choice but to surrender to save Ash's life. Giovanni gets his hands on the Revealing Glass, causing his darkest impulses to surface. Suddenly, Giovanni no longer wanted to conquer the Unova region but wanted to destroy it and ordered the legendary Pokémon Landorus, Thundurus and Tornadus to accomplish that goal. Jessie and James are able to free him from the Reveal Glass, leaving even Giovanni shocked by his own actions.
Giovanni is used very sparingly in the Pokémon anime, with these two occasions marking his only main antagonistic role in the series, and both times he threatens people and Pokémon with death without hesitation. It's clear that Giovanni is considered an enemy because he is simply too dark a character for the unsuspecting. Pokémon animated series, when he's really allowed to let loose, he proves to be its most fearsome opponent.