"That cannot be. You said we were partners. We stood as equals."
"You were created by humans to obey humans. You could never be our equal."
-Mewtwo & Giovanni; Mewtwo Strikes Back
One of Giovanni's greatest achievements was the creation of Mewtwo, a Pokemon cloned from the rarest Pokemon, Mew, but built to be stronger in every way. Mewtwo, the legendary Pokemon, could only have been if for Giovanni's brilliant, yet twisted, plan. The game eludes to the scientists that had created Mewtwo but it was never outright stated, which was a nice subtle touch. When walking through the ruined Pokemon Mansion on Cinnibar Island, there are books and diaries that contain writings about a strange Pokemon. It is thought that in the game Blaine and Mr. Fuji were the culprits who did experiements on it, where in the movie it was infact Scientists whom Giovanni had paid to do this work for him.
After many failed attempts they were able to create "the most Powerful Pokemon", Mewtwo. The scientist had struggled also to recreate his deceased daughter along with three other Pokemon: Charmander, Squirtle, Bulbasaur. Mewtwo was friends with her in a strange dreamworld. She never became a reality but Mewtwo then later used the three Pokemon as his "super clones". Mewtwo was angry and confused when he first awoke and, like in the game, went berserk and destroyed the lab. It was only until Giovanni came and was able to manipulate him with his words that he was able to control him, at least for a little while.
"We dreamed of creating the most powerful Pokemon...and we succeeded."
Giovanni was quick with his wit and had a sharp tounge. He was able to soothe Mewtwo and talk him into being his "Partner". "I see you as a valuable partner." He then tells Mewtwo that he needs to learn how to control his powers and that he [Giovanni] can help him to do so. In this way, he is able to gain Mewtwo's trust and acceptance. "Together with your Psychic Powers and my resources, together, we could control the world." Giovanni says these things but he does not realize that though these are his own intentions, he is feeding them into Mewtwo's mind, and that he would soon become independent of his will.
Giovanni then tricks Mewtwo into wearing Cyber armor. This armor is made to compress Mewtwo's abilities so that Giovanni would be able to tame him and keep his wild abilities at bay. This must have been Giovanni's peak of his career. He was able to manipulate this extremely powerful Pokemon and to him, he became merely a toy. He was used in training is grunts as well as Gym battles. A crossover to the movie is in episode 68 where Giovanni uses Mewtwo to crush Gary. Gary, in fear, tells Ash that this Pokemon was "evil". Being persuaded and brought up by the world's number one criminal mastermind would indeed make his intentions "evil". We find out, however, that Mewtwo is not purely evil. He finds that the cyber armor restrains him and he is still confused about his purpose. One day he calls to Giovanni:
"...what is my purpose?"
"You were made to serve me, that is your purpose!"
Here Giovanni tells us that he was behind the creation of Mewtwo. Mewtwo is in shock, he cries: "But you said we were partners!" Giovanni finally admits to him, in his pride, that Pokemon and People could never be equal. His true intentions shine through, perhaps this was a mistake on Giovanni's part, for as he said that Mewtwo explodes yet again. He breaks free of the armor and flies away, leaving Giovanni and Viridian City behind.
Several years later... Giovanni has not forgotten about Mewtwo, unlike our heroes, his memory was never erased because he was never on Mewtwo's island. For years he has been seeking Mewtwo to gain him back in his custody so that his plans for World Domination could be fulfilled. He finds now that Mewtwo had fled to a Mountainous island near Johto that is protected by rapid fluxuations in weather and winds. Giovanni employs his beloved grunt Domino to take care of the task of finding Mewtwo.
This time, Giovanni is prepare with all sorts of weapons at his disposal and brings out a huge Rocket army to face Mewtwo. He realizes that Mewtwo's personality has softened due to his meeting with Ash in the first movie. Ash tells teaches Mewtwo that there is no reason to fight just because they were all made or born differently. Mewtwo faces Mew and finds that they have more incommon than he had realized and that his purpose in life is to promote peace. Therefore, when Giovanni threatens to harm the Pokemon on the island, Mewtwo quickly caves in and offers himself in their stead. Giovanni thinks and feels that has won until the other Pokemon rise up to defend Mewtwo. Mewtwo retreats inside of the island and sends Giovanni back to his base, whiping out all of his memories. Now Mewtwo is gone for good.
Mewtwo was Giovanni's ultimate weapon and was going to be used to help him find his goal, but as all villains, his master plan had to be foiled. Now, with Mewtwo gone and Team Rocket disbanded in other versions, what does Giovanni have left? And who is the legend when the Mastermind creates the one who is just as intelligent and manipulative as he?