Perhaps in the fanfiction, Zeref discovers that baby Natsu has a hidden power that could either be a great threat or a great asset in his grand plans. This could lead to Zeref trying to either control or protect Natsu.
One idea could be that baby Natsu has some sort of special connection to Zeref that even Zeref doesn't fully understand at first. Maybe Natsu's presence starts to change Zeref's dark thoughts a bit.
One plot idea could be that Zeref discovers a way to reverse his curse through Natsu. Since Natsu is his creation, there might be some hidden connection that could be explored. Maybe Zeref tries to use Natsu's unique dragon - slayer magic to break the chains of his dark magic.
Well, it depends on the specific fanfiction. Some might have a plot centered around their unique friendship in a different AU (alternate universe), like they team up to fight a common enemy. Others could explore their relationship in a more emotional way, perhaps with Zeref having to deal with her new female form and Natsu being there to support her in ways different from the original story.
One idea could be exploring their childhood before they were separated. Maybe Zeref was protective of Natsu and taught him some basic magic skills in secret. Another could be a story where Natsu discovers his relation to Zeref during a really tough battle and has to deal with the emotional turmoil of it. For example, he might hesitate to fight Zeref as fiercely when he realizes they are brothers.
One idea could be that Natsu and Lucy accidentally end up taking care of a baby dragon. Natsu would be excited to teach it fire - breathing tricks while Lucy would be more focused on keeping it safe and fed. Another plot could involve a magic spell gone wrong that turns them into babies themselves, and they have to figure out how to reverse it while in this state. It could also be a story where they find a lost baby in the forest during one of their quests, and they decide to raise it together, which would show their growth as characters in terms of responsibility.
One interesting plotline could be a redemption arc for Zeref. In this, Natsu plays a key role in helping Zeref see the good in the world again. Maybe Natsu shows Zeref the value of friendship and family through his own relationships in the guild. This could lead to Zeref using his powers for good instead of his previous evil - doings.
Well, perhaps Zeref kidnaps Natsu because he sees Natsu as a key to some grand plan. Maybe he wants to use Natsu's power for his own dark purposes. For example, Zeref might think Natsu's unique magic can help him break some sort of ancient curse or gain access to a powerful magic source.
Well, one possible plot could be that Zeref kidnaps Natsu in an attempt to use his power for some dark purpose. Maybe he wants to turn Natsu into a weapon against Fairy Tail. Zeref might believe that Natsu's unique dragon - slayer magic can be harnessed in a way that no one else's can.
It could be another dark mage who sees the potential in baby Natsu and wants to use him for evil purposes. This mage might view Zeref as an obstacle in getting to Natsu.
A possible plot idea is that Zeref is cursed, and Lucy, with her kind heart, tries to find a way to break the curse. Along the way, they face many challenges together, and their relationship evolves from distrust to mutual understanding and perhaps even love. They might also encounter other Fairy Tail characters who are initially against their association due to Zeref's reputation.
One idea could be that Natsu discovers a new and rare type of fairy magic that he has to learn to control. Another could be Natsu getting involved in a fairy war and having to choose a side. Maybe he could also meet a fairy who has the power to grant wishes and he has to decide what to wish for.