Plus they replaced the outstanding Main Mission set with the Command Centre. I don't know if we ever got an on-screen explanation for that.
There was no onscreen explanation for the move from the large Main Mission( with abundant lunar windows to see out) to small Command Center( without any lunar windows to look out). Alpha Moonbase Main Mission is to Command Center what in STAR TREK the Starship Bridge is the BattleBridge.
In SPACE:1999, season 1 with the majority of the sets having lunar windows to see out because of their respective location at upper levels of the Alpha Moonbase. However, in season 2 had all but a few sets without lunar windows at all due to their respective locations below the lunar surface on the lower levels of the Alpha Moonbase.
Read somewhere that the supposed reason for the change (but as you say nothing onscreen so it's apocrphal) was the main mission was located at a high point on Alpha and was was a tad too exposed when the alien nasties were around so it was abandoned).
There's also the often quoted line from Morse regarding his departure, who later claimed he was happy to leave and said "I would rather play with grown-ups for a while."
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