Update: 1.5 fixed it. Got through the scenario, thanks!
Sharkie is right, I'm close to the end of the game but there are a couple game breaking bugs.
Here it is, at last: Marathon TROJAN. Now compatible with Aleph One (1.3 or newer), this uses the native M1 files to deliver the original, unaltered experience we know from the 90's.
M1 compatible fullscreen HUD plugins will work with TROJAN if you don't want to use the included Classic HUD plugin.
Additional files include the Weapons Pump Patch, FAQ, Manual, Spoiler Guide, and read me's from older versions of TROJAN.
Special thank you to Hamish Sanderson for giving us permission to distribute this re-release of TROJAN. Enjoy!