If the databases share server, have a login that has priveleges to both of the databases, and simply have a query run similiar to:
$query = $this->db->query("
SELECT t1.*, t2.id
FROM `database1`.`table1` AS t1, `database2`.`table2` AS t2
");
Otherwise I think you might have to run the 2 queries separately and fix the logic afterwards.