# He will run

Here the word "he" refers to the person who unintentionally killed someone.

# explain his case to the elders of that city

"convince the elders of that city that he had not intentionally killed the person.

# Then they will take him

The word "they" refers to the elders and "him" refers to the person who unintentionally killed someone.

# live among them

This refers to the city as a whole, not to the elders only.