<?php
$data_operation = $this->pdo('select * from operations, users_operations where operations.id = users_operations.id_operation &&  = ?', [
    $this->id
])->fetchAll(PDO::FETCH_OBJ);

$data_mission = $this->pdo('select * from missions, users_operations where missions.id = users_missions.id_mission && users_missions.id_user = ?', [
    $this->id
])->fetchAll(PDO::FETCH_OBJ);

$this->set(compact('data_operation', 'data_mission'));



<?php foreach ($data_operation as $key => $operation) : ?>
    <!--вывод операций-->
    <?php
    $mission_array = [];
    foreach ($data_mission as $v) {
    if ($v->id_operation == $operation->id){
?>
  <!--вывод миссий операций-->
<?
    }

    }
    ?>

<?php endforeach; ?>
---------
<?php
$data = $this->pdo('select {только то что юзаешь и если дублируется делаешь алиасы} from missions m left join users_operations uo on u.id=uo.id_mission left join operations o on o.id=uo.id_operation where uo.id_user=?', [
    $this->id
])->fetchAll(PDO::FETCH_OBJ);
$lastOpID=0;
foreach($data as $item){
if($item->operation_id!=$lastOpId){
//operations
$lastOpId=$item->operation_id;
}else{
//missions

}


}