$arr = [
    '/category0/subcat1/subcat2',
    '/category0/subcat1/subcat4',
    '/category0/subcat5/subcat6',
    '/category2/subcat7/subcat8',
    '/category2/subcat9/subcat10',
    '/category2/subcat11/subcat12',
];

$t = [];
foreach ($arr as $item) {
    $s = explode('/', $item);
    $i = $s[1];
    unset ($s[1], $s[0]);
    if (!$t[$i] ){
        $t[$i] = [];
    }
    foreach ($s as $item){
        array_push ( $t[$i],$item);
    }
}
foreach ($t as &$item){
    $item = array_unique($item);
}
echo('<pre>');
var_dump($t);
var_dump(json_encode($t));
echo('<pre>');