This part of the final phase is only a beginning (5)
I believe the answer is:
alpha
'a beginning' is the definition.
(alpha is a kind of beginning)
'this part of the final phase is' is the wordplay.
'this part of' says the answer is hidden in the clue.
'ALPHA' is hidden in the letters of 'final phase is'.
'only' is the link.
I am not very happy about this link. It may be part of another bit of the clue.
Can you help me to learn more?
(Other definitions for alpha that I've seen before include "First-rate" , "First letter of the Greek alphabet" , "very good rating" , "Beginning" , "Top grade" .)