Obviously, Counter Guardian Emiya is one of the main characters. He will be at the center of the story, driving the plot with his actions and decisions. There could also be characters from the world he is crossing over into. For instance, if it's a crossover with a popular shonen anime world, there might be the protagonist of that world who will interact with Emiya.
Supporting characters from the 'Fate' series might also make an appearance. Characters like Rin Tohsaka or Archer could be involved. Their relationships with Emiya add depth to the story. In the crossover aspect, perhaps there are side characters from the other universe who play important roles in helping or hindering Emiya's journey.
It's possible that antagonists from both the 'Fate' universe and the crossover universe are main characters too. They could be working together or separately against Emiya. For example, an evil mage from the 'Fate' world and a powerful villain from the crossover world might team up to stop Emiya from achieving his goals.
Chapter 368, "You Don't Deserve to Be My Mother", is the clearest early answer because it turns Lin Manru's situation into a concrete plot event. A useful checkpoint is the way the scene starts with I haven't detained anyone, how could I possibly detain him?
Chapter 471, "This is What Happens When You Abandon Sister Li!", is the clearest early answer because it turns Shang Shuyue's situation into a concrete plot event.
Chapter 538, "You Won't Get Angry No Matter What I Ask, Right?", is the clearest early answer because it turns Shang Shaojing's situation into a concrete plot event. The chapter gives readers a real answer by opening on Su Yinwan couldn't ignore Jiang Cheng's unusual behavior any longer...
Chapter 725, "Still Want to be the Second Young Master of the Jiang Family!", is the clearest early answer because it turns Lin Manru's situation into a concrete plot event. The chapter gives readers a real answer by opening on Though Rong Jusheng is known for being righteous, he's anything but...
Chapter 698, "Brother Yan Was Just Forced!", is the clearest early answer because it turns Shang Shuyue's situation into a concrete plot event. The chapter turns that into something concrete by moving from Jiang Li immediately asked for some tools and colored paints.
Chapter 576, "The Electronic Pickles are Gone!", is the clearest early answer because it turns Ai Xiaochun's situation into a concrete plot event. A useful checkpoint is the way the scene starts with Tonight, Team Q exceptionally didn't cook.
Chapter 575, "The First Time Threatening Someone Feels Quite Marvelous", is the clearest early answer because it turns Sis's situation into a concrete plot event. The chapter turns that into something concrete by moving from Is there really no way to get any money out?" After some...
Chapter 731, "Ye Chu Died", is the clearest early answer because it turns Bai Lu's situation into a concrete plot event. It opens with Dean, can I really not do it? and closes on She'd been acting off these days.. The key payoff is that the chapter closes with "Why did you come to the sanatorium?
Chapter 707, "I am Daoist Qingfeng", is the clearest early answer because it turns Jiang Li's situation into a concrete plot event. The chapter turns that into something concrete by moving from Su Yinwan hadn't finished her dessert but, feeling agitated, had...
Chapter 797, "Bu Fan and Bu Chen", is the clearest early answer because it turns Bu Fan's situation into a concrete plot event. It opens with The night grew deeper, and while waiting for news, Jiang Li dragged...