This mod has a LONG list of problems. I'm not sure if it's supposed to be fully playable start to finish, but it isn't. Progression get's hard bottlenecked at two major points, both of which are broken.
First up, Examination Room. Exam rooms don't actually drop in game, it's a vanilla issue. And yet without them progression get's stalled because you need Biolabs.
Second, the old battleship mission. It wont spawn. I tried editing it to have a 100% chance to spawn, but it failed to do so. And yes I have the wreck but not the codes. I tried fixing the spawnZone to 3, which it should be, and the game outright crashes at the end of the month. Without this event, the last story events can't fire, and thus the game can't be completed.
Edit: Warboy said he got it to spawn by making the change, without a crash. Thus my change of 100% chance for Naga and removing the timeout may have caused the crash. Which means the Naga Temple is broken.
Third, the Naga Temple. I never saw this mission. Because it only has a 50% chance to spawn each month, and you must have a Naga Squad Leader researched. AND all before month 8, when it can never spawn again. It already has a 'do not spawn if' trigger in the Trident research. There should be no reason this mission has a timeout factor as well.
Lastly, Sonic weapons are broken, can't be used at all. You forgot to set the environment flag for them. Strangely Aliens can still use them. As are Advanced Medkits. They require a bad string, which doesn't exist. So they can't be built.
Moving on from what is broken, we have balance. First up, the Biolab. Biolabs are more expensive, have more maintenance, and give less labspace. And you MUST have them to build certain items or research certain tech. I get you nerfed labspace all around, but Biolabs should give the same amount, if not more. They're supposed to be upgraded labs after all.
Next up, Aqua Jet Torpedos. I'm not looking at their combat stats, I'm looking at their sell value. These things sell for so much a single workshop devoted to doing nothing but building and selling them can pay for entire bases, with extra. And you can get their rather early on. It's so silly that they sell for even more than Gauss Cannons, which are impossible to get without cheating due to the exam room issue.
Next, Acid Rifle. What is the point of this weapon? Ever base game alien is utterly immune. I'm thinking that was a typo. You have Lobstermen, who take 10% more smoke damage, but are immune to acid? That might have been backwards. As far as I know, smoke doesn't even work in TFTD, at least not underwater.
Lastly, the Sonic Sniper Rifle. It has less accuracy, and less damage, than a Heavy Sonic. For the same TU cost. I get that it removes 1/3 armor. But in TFTD armor is NOT a major issue. The Triscene, which has the most armor in the game, does NOT require this weapon. Sure it's frontal/around armor is 144/132 respectively, but it's under armor is a mere 10. And being a 4x unit it takes 4x damage from explosions. A single sonic pulsar, doing MINIMUM damage, will one shot it. The Xarquid's 60 armor is the next highest. Except that only taking off 1/3 means you remove 20 armor. And a Heavy Sonic's 130 damage, 40 more than Sniper's 90, will ALWAYS do more damage. There is literally no situation where a Sonic Sniper Rifle will have meaningful impact. By the time you can research it you already have sonic pulsars and Heavy Sonic. At least the Sonic Autogun can justify itself by firing off 3 shots of 105 damage. That gives you a potential way to kill Lobstermen at range, something few other things do.
