In some cases, it could be the environment itself. For instance, if they are in a highly dangerous and unforgiving area, like a collapsing building or a toxic zone, and Ellis makes a wrong move trying to lead the group through, which leads to his death.
Perhaps in the fan fiction, Ellis is bitten while trying to protect a vulnerable member of the group. He then decides to isolate himself to avoid turning and ends up dying alone.
A new character entirely could be the main antagonist. For instance, an alien - like being from a far - off land who comes to the ninja world with the sole intention of destroying it. Naruto, being the strongest ninja, stands in their way and ultimately pays the price with his life.
One common theme is the idea of redemption. Since Hunter is a somewhat 'evil' or at least dangerous creature in the game, many fanfictions explore his journey towards redemption through his relationship with Ellis. Another theme is friendship. They come from different 'sides' but form a bond that defies expectations.
It could be a super intelligent pirate who has been secretly controlling events in the One Piece world. This antagonist might be several steps ahead of everyone, creating elaborate plans to take over the Grand Line. Luffy, with his newfound intelligence, has to match wits with this foe.
The main antagonist could be a mean-spirited mole. This mole is constantly digging tunnels under the garden and causing chaos. He doesn't like Gnomeo and Juliet's love because he believes it's disrupting the natural order of the garden. He tries to separate them by causing misunderstandings between their families.
An organization that believes in using Pokemon for dark magic could be the main bad guy. They see Iris and her Pokemon as a threat to their plans, so they constantly try to stop her. They might have their own powerful, corrupted Pokemon that they use to battle Iris. They could also be stealing Pokemon from other trainers to use in their dark experiments.
A rival medicine cat from another Clan might be the main antagonist. They could see Alderheart as a threat to their own status or the well - being of their Clan. So they might use dark magic or some underhanded tactics to bring about his death.
A dark and mysterious sorcerer could also be the main antagonist. The sorcerer has a long - standing grudge against Byakuya's family or the place he protects. Using dark magic, the sorcerer sets up a series of deadly traps and curses, which ultimately lead to Byakuya's death.
The main antagonist could still be Voldemort. After all, he is the main source of danger for Harry in the original series. L would then be pitted against Voldemort's dark magic and his army of Death Eaters. L would have to use his wits and any new abilities he might have in this fanfic to outmaneuver Voldemort and keep Harry safe.
It could be a rival politician who sees Trump's association with Grimace as a threat. This rival might try to spread false rumors about Grimace being a dangerous or untrustworthy being, just to undermine Trump.