Thank you for clearing it up. I did some research beforehand as well

"Extinction Event Horizon" by alex_mmc. I don't know why it is excluded in original mod description. Maybe it is kind of 'bonus map'.

Which campaign is "ep1_eeh" a part of?

Add-on updated. As I said in the change log, this will only affect player who unchecked 'Give weapons on spawn'.

I'll update the add-on.

PS. The author said "Map is possible to compelete without any firearms at all.", so current behavior is also technically valid :)

On ep1_eeh, player receives starting weapons through point_servercommand entity. It's blocked in GMod, which makes player unable to progress without giving themselves a weapon through spawnmenu.
You might want to make a script that spawns these on player's position: weapon_physcannon, weapon_stunstick, weapon_smg1, weapon_pistol and item_suit

I figured out why this inconsistency happens. First gunship doesn't move to next path. Unfortunately, I can't solve this issue. FP must fix it.

At least, this is just a visual problem, not a game breaking problem. I'll leave it as is, until FP fixes it.

I misread the map I/O. Here is workflow of three gunships.

When you move from starting point, first gunship will be activated, but this is for visual. It cannot attack player, and is forced to move along with designated path.

When you take a ladder to the rooftop and go outside, second gunship will be activated. It knows where you are and will attack you. It is not invulnerable, but you don't have proper weapon to kill it. This second gunship will be removed when you go down to the hole in the building.

When you go down and pass certain trigger, third gunship will be activated. It also knows where you are, and will attack through thin wall like window above. This final gunship will be removed when you press elevator button.

So, you should see one gunship at once through the map. I will check the map in this add-on.

For me it appeared right as soon the map began, plus if that one's meant to be killed when you get up to the roof then I never found a way up there because the layout didn't ever seem to go up there.

I just replayed the mod for investigation.

According to the map, you should encounter one gunship when on rooftop, and two gunships at the last part of the map. The first gunship should be 'killed' when you leave the rooftop.
But in my playthrough, the first gunship didn't get 'killed', and other two gunship didn't get activated. I think either I skipped some trigger when testing, or GMod executes the intended behavior of the map correctly.

So, the Gunship you first see in Direwolf, is that supposed to just hang around the entire time? Because it gets pretty confusing when you have two Gunships except only one is attacking you because the other is likely just part of a scene that isn't despawning.