UPDATE:
Sorted it.
Needed a tax_query
End result that allowed me to filter archive based on the taxonomy:
// Filter by Taxonomy when needed.
if ($_GET['discipline']) :
$term = get_query_var('discipline');
$args = array(
'post_type' => 'case_study',
'tax_query' => array(
array(
'taxonomy' => 'discipline',
'field' => 'slug',
'terms' => $term,
)
)
);
else :
// show everything
$args = array(
'numberposts' => -1,
'post_type' => 'case_study',
);
endif;