As far as I know, there are two ports of this game for MorphOS, one old one created by Bigfoot, the other newer one by BSzili. I don't know if any of them will work with mods, you'll have to check.
Quake 2 3.21 by Bigfoot]
Yamagi Quake 2 4.90 by BSzili.
MorphOS.pl
PowerBook G4 1.67GHz|2GB DDR2|ATI Radeon 9700M 128MB|SSD 80GB|TFT 17"|MorphOS 3.1x
Alienware 15 R3|WinUAE 5.x/AmigaOS4.1x & Icaros Desktop 2.x & QEmu 9.x.x