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The choice of tenses usually reflects the speaker's sense of the sequence of events. The speaker may forget to say something that explains a shift of tense: he is thinking it but not saying it. In the passage above, one gets the impression that they came up with the script after they had begun filming. That might have been the case. The script might have evolved during the filming.

McLaren had intended the film to be extreme. He had begun filming using Russ Meyer (who produced sordid and exploitative films) and the script (the one he and Meyer came up with) reflected this intention.

What is clear is that the intention precedes everything, including the script:

McLaren had intended the film to be extreme. ... The script (the one he and Meyer came up with) reflected this intention.

We're not sure what to make of the past perfect here:

He had begun filming using Russ Meyer...

The simple past might be better there.

McClaren had intended the film to be extreme. He began filming using Russ Meyer and the script he and Meyer came up with reflected this intention.

The choice of tenses usually reflects the speaker's sense of the sequence of events. The speaker may forget to say something that explains a shift of tense: he is thinking it but not saying it. In the passage above, one gets the impression that they came up with the script after they had begun filming. That might have been the case. The script might have evolved during the filming.

McLaren had intended the film to be extreme. He had begun filming using Russ Meyer (who produced sordid and exploitative films) and the script (the one he and Meyer came up with) reflected this intention.

The choice of tenses usually reflects the speaker's sense of the sequence of events. The speaker may forget to say something that explains a shift of tense: he is thinking it but not saying it. In the passage above, one gets the impression that they came up with the script after they had begun filming. That might have been the case. The script might have evolved during the filming.

McLaren had intended the film to be extreme. He had begun filming using Russ Meyer (who produced sordid and exploitative films) and the script (the one he and Meyer came up with) reflected this intention.

What is clear is that the intention precedes everything, including the script:

McLaren had intended the film to be extreme. ... The script (the one he and Meyer came up with) reflected this intention.

We're not sure what to make of the past perfect here:

He had begun filming using Russ Meyer...

The simple past might be better there.

McClaren had intended the film to be extreme. He began filming using Russ Meyer and the script he and Meyer came up with reflected this intention.

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The choice of tenses usually reflects the speaker's sense of the sequence of events. The speaker may forget to say something that explains a shift of tense: he is thinking it but not saying it. In the passage above, one gets the impression that they came up with the script after they had begun filming. That might have been the case. The script might have evolved during the filming.

McLaren had intended the film to be extreme. He had begun filming using Russ Meyer (who produced sordid and exploitative films) and the script (the one he and Meyer came up with) reflected this intention.