This is based on a little headcanon I have. I don't own any rights to any of the Professor Layton franchise. Enjoy!
Flora had been meaning to tell the Professor for a while now. However, every time she tried to, something would happen and the moment would be gone. It was something she knew she should definitely be afraid of, but something inside her just wouldn't allow her to fear it the way she felt she should. Maybe her fearlessness came from being by the Professor and knowing that no matter what happened, he could always protect her. Or maybe it was because it had been going on for so long that it almost felt familiar- too familiar to be considered a threat anymore. After all, if they really wanted to hurt them they would have done so by now. But they seemed content with just sitting and watching them from afar. And that didn't seem like a very threatening thing.
The truth was, the Professor had shadows. But not just the kind that appeared in light. No, these shadows were mysterious figures that lurked around corners. They followed them everywhere the Professor went; always half a step behind. She had never actually properly seen any of these shadows but she had always felt their presence ever since she had first laid eyes on the Professor and Luke in St Mystere. But, Flora had managed to catch a glimpse of a couple of them. The first time was when they had been in the quiet village of Dropstone during their search for the Elysian Box before Flora got herself kidnapped by Don Paolo (she still resented herself for not seeing that coming). Luke had become captivated by a certain stool selling soft toys and managed to drag Flora and the Professor over to it. While Luke had his hand gently wrapped around Flora's wrist, she giggled and tried not to stumble as he tugged on her arm slightly, signally for her to follow him. Her eyes flickered up for a moment and that's when she caught her first glimpse at one of the shadows that followed Layton so carefully. Through the crowd, she saw a man stood on the corner of the street. He was gone almost as once as her gaze hit him but she managed to make out a white mask that covered his eyes, a white feather boa wrapped around his neck, and a grey cloak that flared out slightly when the man quickly slipped behind the corner once Flora had looked up. She shook her head slightly as though waking from a dream. But she was brought back to reality by another tug on her arm from Luke and she let out a laugh and allowed herself to be pulled away towards the stall. What she had witnessed would soon be long gone from her thoughts but would always remain in her memories.
The second time was during their time in 'Future London'. Flora had followed them to the 'future' and when they saw her, the Professor and Luke had no choice but to take her along with them. At the time Flora saw the shadow, they were exploring China Town with Clive- or, as they knew him at the time, future Luke. The rest of the group were focused on the task ahead but Flora couldn't help but constantly look around in complete awe. She still hadn't quite wrapped her head around the fact that they were in the future. Everything was just so fascinating and eye catching and she didn't understand why they couldn't go exploring for just five minutes. The group were walking around, trying to gather information from the locals when Flora caught a glimpse of the shadow. This one was different from the last one she saw in Dropstone. Flora was almost certain this shadow was a woman. She had long, brown, slightly curly hair and wore a bright yellow jacket. She couldn't fully take in her appearance because as soon as she blinked, the shadow had gone, disappearing into one of the shops. Curiosity taking over, Flora quietly crept away from her friends and entered the shop the shadow had just gone into. But when she opened the door, there was no one inside but an old man who Flora assumed was the shopkeeper; no signs of the yellow-clad woman. With a defeated sigh, Flora slipped back out of the shop and made her way back to her friends, hoping no one had noticed her absence.
Once Luke moved away to America, Flora slowly felt the presence of the shadows slip away; as though they were realising it was time to move on. Flora often wondered if the Professor knew about them and never said anything, or if he really never noticed he was being followed all this time. She never saw them again, but sometimes she would feel their presence for the briefest of moments when they were out on another adventure. And it never failed to make her smile.