Well, he might be used as a bargaining chip against the Whitebeard Pirates. His captors could try to extract information about the pirates' secrets or hidden treasures.
It could be the Blackbeard Pirates. Since they have a history with the Whitebeard Pirates, they might capture Marco to get information or as a form of revenge.
Perhaps Marco uses his intelligence to outwit his captors. He could pretend to be weak or injured and when they least expect it, he could make his move. He has a lot of experience from his time with Whitebeard, so he could use that knowledge to find a weakness in their security and escape.
Another possibility is that a rival pirate group that has a long - standing feud with the Whitebeard Pirates managed to finally get the upper hand and capture Marco. They could have been studying his movements for a long time and found a weakness in his defenses. This group might be led by a very cunning and powerful pirate captain who has a personal vendetta against the Whitebeard Pirates and sees capturing Marco as a major victory.
One possible scenario in this fanfiction could be that Ace and Marco are facing a powerful and unknown enemy in a spooky, haunted island. The island is filled with strange noises and dark shadows. Ace's fire powers seem to be ineffective against this new threat as it keeps disappearing and reappearing. Marco, with his phoenix abilities, tries to scout from the air but gets caught in some sort of dark mist. They have to rely on each other and their friendship to overcome their fear and find a way to defeat this mysterious foe.
It could be that they are trapped in a dark dimension. Here, the laws of the normal world don't apply. Ace tries to create fire, but it turns into ice instead. Marco's wings start to freeze when he tries to fly. They are surrounded by strange creatures that seem to be made of pure darkness. They have to work together to find a portal that will take them back to their world. Ace uses his intuition and Marco uses his knowledge of the One Piece world to search for clues on how to escape.
A common theme is friendship. Since Marco is an important character in One Piece, in fanfiction with a female character, they often form a strong bond. They might start as strangers and gradually become comrades who trust each other implicitly.
Growth is a prevalent theme. As they go through various battles and experiences in the fanfictions, they grow both as individuals and in their relationship. Their understanding of each other and their own abilities develops. Additionally, the theme of brotherhood is strong. They are like brothers in the crew, and this brotherly love is often a central focus in these fanfictions.
One common theme is friendship. Given Luffy's nature of making strong bonds with people, fanfictions often explore how he and Marco could form a deep friendship. Another theme could be adventure. They are both from the 'One Piece' world which is full of adventures, so fanfictions might create new and exciting adventures for them to go on together.
Maybe it's a cold night at sea. Ace, who's not used to the cold as much as Marco, huddles up to him. Marco, being the kind-hearted person he is, just pulls Ace closer. They start reminiscing about their adventures and friends, creating a really warm and fuzzy moment.