The pilots knew their mission was to divert aircraft, but did not know that the threat came from hijacked airliners.
( ( The pilots ) ( ( ( ( ( knew ( ( their mission ) ( was ( to ( divert aircraft ) ) ) ) ) , ) but ) ( ( did not ) ( know ( that ( ( the threat ) ( came ( from ( hijacked airliners ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NNS pilots)) (VP (VP (VBD knew) (SBAR (S (NP (PRP$ their) (NN mission)) (VP (VBD was) (S (VP (TO to) (VP (VB divert) (NP (NN aircraft))))))))) (, ,) (CC but) (VP (VBD did) (RB not) (VP (VB know) (SBAR (IN that) (S (NP (DT the) (NN threat)) (VP (VBD came) (PP (IN from) (NP (JJ hijacked) (NNS airliners))))))))) (. .)))
The pilots were on high alert, due to the hijacked aircraft.
( ( The pilots ) ( ( were ( ( ( on ( high alert ) ) ( , due ) ) ( to ( the ( hijacked aircraft ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NNS pilots)) (VP (VBD were) (ADJP (ADJP (PP (IN on) (NP (JJ high) (NN alert))) (, ,) (JJ due)) (PP (TO to) (NP (DT the) (JJ hijacked) (NN aircraft))))) (. .)))