He drapes the altar cloth around her shoulders, places his headphones over her ears and sits beside her with his arm around her to comfort her.
A bit later, Arai calls Misuzu to see if the two made it back and the hosts learn about what transpired after they left.
Flashback to Haruhi and Arai in middle school discussing Haruhi's plan to take the entrance exam for Ouran Academy.
Though Arai makes it clear that he wishes they could attend the same high school, Haruhi is clueless and misinterprets all of his statements as generic; essentially dismissing him as a potential boyfriend.
When Hikaru asks how she can tell he's upset about Kaoru, she says she just can; the fact being that it is Haruhi's attention to details regarding her friends that enables her to know them so well.
The moment Haruhi "includes" Kaoru, the date begins to improve and the hosts leave them alone.