One of two I encountered in upper atmosphere (6)
I believe the answer is:
either
'one of two' is the definition.
(one of two options)
'i encountered in upper atmosphere' is the wordplay.
'encountered in' indicates putting letters inside.
'upper atmosphere' becomes 'ether' (I've seen this in another clue).
'i' inserted into 'ether' is 'EITHER'.
(Other definitions for either that I've seen before include "Word indicating the following alternatives" , "offered a choice" , "Each of two; moreover" , "could be one of two" , "No matter which (of two)" .)