i'm assuming that you didn't mean to underline "did," right?

assuming that 'did' is not underlined,

idiom is Not X But Y

C and E are wrong

A) 'it' should refer to a noun or thing. here we are talking about an action and hence wrong
B) did so refers to the action specified before - establish a permanent colony
D) 'did not at plymouth' - did what? wrong

ans B.

OA pls?

The answer is B.

C and D are cannot be the answer because there is NO pronoun to refer to the establishment of a colony and something must be there to refer to the phrase.

'It' does not work because 'establishment of a colony' is a verb phrase. "did so" is the appropriate idiomatic usage to refer back to a verb phrase in the past tense, and so it's the best answer choice.