How does Hibernate query on a column with @ManyToOne relationship?

I was wondering, How does hibernate query the table internally when we query on a column which is foreign key. Please see the code for more understanding

Employee Table

@Entity
@Getter
@Setter
@NoArgsConstructor
@AllArgsConstructor
public class Employee {
  @Id
  private String userId;
  
  private String name;
    
  @ManyToOne(fetch = FetchType.EAGER, optional = false)
  @JoinTable(
    name = "department",
    joinColumns = @JoinColumn(name = "employee_id"),
    inverseJoinColumns = @JoinColumn(name = "department_code")
  
  private Department department;
    
}

Department Table

@Data
@Entity
@Builder
@NoArgsConstructor
@AllArgsConstructor
public class Department{
  
  @Id
  @Column(name = "code", unique = true)
  private String code;

  @Column(name = "name", nullable = false)
  private String name;

}

So once the application is deployed, we will have three tables i.e. employee, department and employee_department. Now if I write hibernate like findByDepartmentCodeIn(Department Code) , How will hibernate internally parse this query ? I want to create an index on column department_code to make the former query faster so where do I create an index, in the department table or in the resulting merger employee_department table ?