Maybe Naruto would face a powerful enemy that he can't defeat with his normal jutsu. So, he decides to take on the Batman - like approach of using strategy and gadgets. He could build his own ninja - style gadgets and use them to outwit his foe. This would be a major shift in his usual fighting style.
Well, perhaps in this fanfiction, Naruto is somehow transported to the Batman universe and is neglected by the local heroes at first. He then has to prove himself by using his ninja skills in Gotham's dark alleys, like using his shadow clones to confuse the bad guys and his speed to catch the elusive criminals.
It could be that there is some sort of misinformation spread by an evil organization. They create false evidence that Batman is planning to destroy Naruto's village. Naruto, being the protector of his village, decides to take pre - emptive action. He tracks Batman down and in a fierce battle, kills him. But then as he starts to investigate further, he discovers the truth and has to live with the guilt of killing an innocent (in this case, Batman who was misrepresented).
One plot line might be that Naruto has a secret mission to protect a sacred object that has been hidden from the ninja world. This object could hold the key to some great power or knowledge. He has to keep it a secret from everyone, including his friends, and this creates a lot of internal conflict as he struggles to balance his loyalty to his friends and his duty to protect the object.
One possible plot line could be that Naruto discovers the Light Hawk Wings as a part of his heritage. He then has to learn how to use them to defend his village from a new, powerful threat.
One plot line could be that Female Naruto accidentally switches bodies with Akamaru. This would lead to a lot of comical situations as she tries to navigate being a dog in the Inuzuka clan. She would have to communicate with Kiba in a different way and also figure out how to use Akamaru's skills to her advantage.
One possible plot could be that Naruto is somehow transported to the Batman's universe. Maybe a villain with reality - warping powers is involved. And the 'lemon' aspect could be a code name for a new, experimental weapon in Gotham that Naruto and Batman have to work together to stop from falling into the wrong hands. They would combine Naruto's ninja skills with Batman's detective and combat abilities.
One possible plot line is that Naruto is injured badly and Tsunade has to use her medical skills to save him. During his recovery, they have deep conversations about life, dreams, and the future of the village. Another could be that Tsunade decides to train Naruto in a special jutsu that only she knows, which would enhance Naruto's abilities greatly.
One plot line could be that Rin somehow gets resurrected and Naruto has to protect her from those who might want to use her for their own gain. Since Rin was a valuable medical ninja, there could be groups that want to force her to heal their injured or create powerful medical jutsus for them.
In a 'Naruto is Batman fanfiction', Naruto could take on Batman's sense of justice. He would be more brooding and serious, much like Batman. Maybe he would even create a secret identity within the village. His costume could be a blend of his usual orange jumpsuit and some elements of Batman's suit, like a cape that has special abilities, like being able to turn invisible or something.
A plot line might involve Athena seeing Percy's potential in a different way than just as a demigod hero. She could be intrigued by his unique combination of courage and loyalty, and her seduction could be an attempt to bring him closer to her side, perhaps to help in some grand plan. Maybe she disguises herself as someone Percy trusts and slowly reels him in with her charm. Or it could start with Athena giving Percy special tasks that lead to them spending more time together, and during this time, the seduction begins.