The structure by the time~, ~

Question

On the Trial of Typhoid MaryCareful research and some clever detective work by Dr.George Soper, sanitary engineer employed by the New York Department of Health, traced the disease to Mary Mallon. Unfortunately, by the time Soper had identified Mallon as the source of infection, she was gone, on to yet another job as a cook or housekeeper.[Source: Reading for Results Ninth Edition by Laraine Flemming]I think "had identified" should be "identified" like the tense that is used in other sentences made of  the structure "by the time~."And I'd like to know if my thought is right.

Fivejedjon · Accepted Answer

It's fine as it is.

Park sang joon · Answer

Thank you, fivejedjon, for your kind answer.

Then I'd like to know if the sentence says after Soper identified Mallon as the source of infection, Mallon went on to yet another job.

Fivejedjon · Answer

No. She moved on to another job before Soper identified her.

Park sang joon · Answer

Thank you, fivejedjon, for your continuing support.

Then, could you please explain to me why the clause use the past perfect tense that begin with "by the time"?

The structure by the time~, ~

On the Trial of Typhoid Mary

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