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.
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.
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 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...
Chapter 703, "Slap Oneself", is the clearest early answer because it turns Jiang Li's situation into a concrete plot event. It opens with Wu Daoshan quietly raised his head to size up Zhao Lang, and sure... and closes on Young Master Gu was intending to back Jiang Li..
Chapter 595, "Four-legged Black Toad", is the clearest early answer because it turns Four-legged Black Toad's situation into a concrete plot event. It opens with Jiang Li steadied himself with support, endured for a while, and then...
Chapter 841, "Isn't this Daniu?", is the clearest early answer because it turns Aunt Zhao's situation into a concrete plot event. The chapter gives readers a real answer by opening on Zhao Lang took the photograph and glanced at it, chuckling, "It...
Chapter 803, "Younger Brother Misses Mom", is the clearest early answer because it turns Mom's situation into a concrete plot event. It opens with Brother, do you think hiding here is a bad idea?" "Don't worry,... and closes on It was as if she had been replaced by a different person..
Chapter 837, "Why did she come?!", is the clearest early answer because it turns Rong Ya's situation into a concrete plot event.