In short, while leaders in Washington believed that the fighters above them had been instructed to take out hostile aircraft, the only orders actually conveyed to the pilots were to ID type and tail.
( ( In short ) ( , ( ( while ( ( leaders ( in Washington ) ) ( believed ( that ( ( ( the fighters ) ( above them ) ) ( had ( been ( instructed ( to ( ( take out ) ( hostile aircraft ) ) ) ) ) ) ) ) ) ) ) ( , ( ( the ( only orders ) ) ( actually ( ( conveyed ( to ( ( the pilots ) ( were ( to ( ID ( ( type and ) tail ) ) ) ) ) ) ) . ) ) ) ) ) ) )
(ROOT (S (PP (IN In) (ADJP (JJ short))) (, ,) (SBAR (IN while) (S (NP (NP (NNS leaders)) (PP (IN in) (NP (NNP Washington)))) (VP (VBD believed) (SBAR (IN that) (S (NP (NP (DT the) (NNS fighters)) (PP (IN above) (NP (PRP them)))) (VP (VBD had) (VP (VBN been) (VP (VBN instructed) (S (VP (TO to) (VP (VB take) (PRT (RP out)) (NP (JJ hostile) (NN aircraft))))))))))))) (, ,) (NP (DT the) (JJ only) (NNS orders)) (ADVP (RB actually)) (VP (VBD conveyed) (SBAR (TO to) (S (NP (DT the) (NNS pilots)) (VP (VBD were) (S (VP (TO to) (VP (VB ID) (NP (NN type) (CC and) (NN tail))))))))) (. .)))
As a result, the hijacked planes were allowed to remain in the air.
( ( As ( a result ) ) ( , ( ( the ( hijacked planes ) ) ( ( were ( allowed ( to ( remain ( in ( the air ) ) ) ) ) ) . ) ) ) )
(ROOT (S (PP (IN As) (NP (DT a) (NN result))) (, ,) (NP (DT the) (JJ hijacked) (NNS planes)) (VP (VBD were) (VP (VBN allowed) (S (VP (TO to) (VP (VB remain) (PP (IN in) (NP (DT the) (NN air)))))))) (. .)))