SELECT `p`.*
FROM `pupils` AS `p`
JOIN `pupils_cities` AS `pc` ON `pc`.`pupil_id` = `p`.`id`
JOIN (
SELECT `city_id`
FROM `pupils_cities`
GROUP BY `city_id`
ORDER BY COUNT(*) DESC
LIMIT 1
) AS `cnt` ON `cnt`.`city_id` = `pc`.`city_id`