Lily and James Potter could still be important characters. Their friends might be reflecting on their sacrifice and the loss of their son. Maybe through flashbacks or the way their friends remember them, they would play a role in the story.
Voldemort would surely be a main character. With Harry dead as a baby, Voldemort's actions and how he further consolidates his power would be a major part of the story.
Sirius Black could be a central figure. He was Harry's godfather and his anger and grief over Harry's death could drive his actions. He might be on a quest for revenge against Voldemort or trying to protect those that Harry was supposed to protect in the original story.
Megatron could also be a major character. Maybe he views Harry Potter as a threat to his power and plans. He could try to either destroy Harry or use his unique abilities for his own evil purposes. And then there could be Bumblebee, who befriends Harry and helps him communicate with the other Autobots, since Bumblebee is often good at making connections.
There could be a doll collector named Alice. She might be Harry's friend or rival, always competing to get the best dolls in the story.
Hermione could be a main character. She might be the one who helps Harry understand and control his gorgon powers. For example, she could research in the library to find ancient spells or potions that can suppress the gorgon - like effects when they are unwanted.
There might also be a love interest for Harry. This character could be someone who is also involved in the dangerous world of assassination in some way. She or he might be a fellow assassin or someone who is on the periphery of that world but still gets drawn into Harry's life, adding a romantic sub - plot to the story.
There could be the mafia boss. He might be a tough and shrewd character who takes Harry under his wing at first but later becomes suspicious of Harry's actions. Another main character could be Harry's best friend in the mafia. They go through all the dangerous and exciting adventures together, and this friend might have different views on the mafia life compared to Harry.
There could be original characters created specifically for the fanfiction. For example, a wizard who has some knowledge about the origin of the Omnitrix and tries to guide Harry. This character could be an old hermit - like wizard who has been studying interdimensional objects for years. Also, there might be a villain who is after the Omnitrix, someone who wants to use its power for evil purposes and constantly hunts Harry down.
Perhaps there's a mentor figure, an old and experienced pet trainer who gives Harry advice from time to time. Another possible character could be Harry's rival in the pet training world. This rival might always be trying to outdo Harry in training different pets, which adds some drama to the story.
There could be a range of characters. For instance, there might be a powerful Sith Lord who sees Harry as a threat to the traditional Sith ways because of his neutral stance. On the other hand, there could be a young Jedi who is initially suspicious of Harry but later comes to understand his unique position. There might also be some side characters, like smugglers or bounty hunters, who get involved in the story because of Harry's actions and the power struggle around him.
Perhaps there is a female alien diplomat who tries to negotiate with Harry to stop his tyrannical rule. Also, there could be a group of human astronauts who end up in his space domain and have to either submit to his rule or try to escape. Another character could be an old space wizard who has knowledge of a power that could dethrone Harry and is hunted by his forces.
Besides Harry, death is the central character in this concept. But there could be other magical creatures or beings involved. Maybe thestrals, since they are associated with death in the original Harry Potter lore. They could play a role in facilitating the friendship between Harry and death. And of course, Harry's other friends from Hogwarts, like Neville and Ginny, could also be part of the story, either being curious about or affected by Harry's friendship with death.