Mr. Green is never blackmailed
Regardless of which ending is followed, the only explanation for Mr. Green's presence is that he is not a victim. His homosexuality must be a façade in all three scenarios because nothing else is ever used against him. Nobody even knows anything about Mr. Green until he offers the information, whereas Mr. Boddy holds secrets about every other guest. I imagine that the hidden agent still works for The Federal Bureau Of Investigation in the first two versions of the story but never specifies it because Wadsworth manages to catch the blackmailers and murderers. That is especially suggested in the dinner scene when Mr. Green tells Mrs. Peacock that he recognizes her true identity. His smarmy, mischievous smile indicates that he is aware of what the senator and his wife have been engaging in. He gives another hint upon admitting to Miss Scarlet that he has already known for some time about her illegal business. When applicable, Mr. Green is probably sent to the mansion as back up assistance in case if anything happens to Wadsworth, and to give a secondary report. It is possible that the investigative agency keeps Mr. Green and Wadsworth out of each other's acquaintances so that the latter's shock is genuine when he hears the former's revelation. That helps both men remain undercover and prevents the others from growing suspicious. Most likely, the fact that the chief of the incriminating team does not acknowledge Mr. Green when Miss Scarlet or Mrs. Peacock is arrested is due to not yet having the details on what has occurred in the house during the evening. He can't be sure of who has done or said what, and wants to make certain that he does not annunciate Mr. Green's purpose to the wrong person.
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