The NYT , in its front-page coverage, says the plane was flying far lower than the rules for training missions allow.
( ( The NYT ) ( , ( ( in ( its ( front-page coverage ) ) ) ( , ( ( says ( ( the plane ) ( was ( flying ( ( far lower ) ( than ( ( ( the rules ) ( for ( training missions ) ) ) allow ) ) ) ) ) ) ) . ) ) ) ) )
(ROOT (S (NP (DT The) (NNP NYT)) (, ,) (PP (IN in) (NP (PRP$ its) (JJ front-page) (NN coverage))) (, ,) (VP (VBZ says) (SBAR (S (NP (DT the) (NN plane)) (VP (VBD was) (VP (VBG flying) (ADVP (ADVP (RB far) (JJR lower)) (SBAR (IN than) (S (NP (NP (DT the) (NNS rules)) (PP (IN for) (NP (NN training) (NNS missions)))) (VP (VBP allow)))))))))) (. .)))
The NYT also reported that the plane was shot down on order of the President. 
( ( The NYT ) ( also ( ( reported ( that ( ( the plane ) ( was ( ( shot down ) ( on ( order ( of ( the President ) ) ) ) ) ) ) ) ) . ) ) )
(ROOT (S (NP (DT The) (NNP NYT)) (ADVP (RB also)) (VP (VBD reported) (SBAR (IN that) (S (NP (DT the) (NN plane)) (VP (VBD was) (VP (VBN shot) (PRT (RP down)) (PP (IN on) (NP (NP (NN order)) (PP (IN of) (NP (DT the) (NNP President)))))))))) (. .)))