A short time later Nobunaga arrived in Kyoto to face Yoshiaki but was surrounded by Yoshiaki, whereupon Yoshitaka formed an alliance with his former enemies Nagamasa AZAI and the Miyoshi clan, gathered together his former vassals and waged a guerilla-style battle on Nobunaga's forces in South Omi.
やがて上洛した信長と義昭が対立し、義昭によって信長包囲網が形成されると、義賢は義治と共に仇敵であった浅井長政や三好氏らと手を結び、旧臣をかき集めてゲリラ的に南近江で織田軍と戦った。