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))))))))) (. .)))
The fighters had been ordered to take out all hostile aircraft.
( ( The fighters ) ( ( had ( been ( ordered ( to ( ( take out ) ( all ( hostile aircraft ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NNS fighters)) (VP (VBD had) (VP (VBN been) (VP (VBN ordered) (S (VP (TO to) (VP (VB take) (PRT (RP out)) (NP (DT all) (JJ hostile) (NN aircraft)))))))) (. .)))