How to deal with Ninjas?

[Bananas_Akimbo]

No other early game enemy gives me as much trouble as the fiendish Block Lotus Assassin. I'd rather face Chupacabras at night, at least those I can reaction-shoot. I never manage to finish an outpost mission without losing an agent or a dog if I'm lucky. The only way to even find a ninja is to wait for one to attack me, since their throwing range is significantly higher than my spotting range.
My original plan for the new 1.0 start was to leave the Black Lotus arc to later. Postpone doing outposts and bases until I have at least Bio Exo suits available (with that strong cutting resistance an agent can usually tank a hit or two) but I just can't leave them be. The promise of briefcases full of sweet dosh and flame gloves is just too alluring.

My strategy at the moment is to simply let the dog walk in front of my group of soldiers and hope, that the ninja strikes from that direction and manages to only kill the dog and nobody else. Then get him in the next turn.

Honestly, I am quite baffled by the difficulty of this enemy type compared to others, particularly at this point in the game and even later. Even by late 1998 the only thing I can do is to tank their attack with my improved armour and then retaliate. The presence of assassins in any mission makes it significantly harder than corresponding missions of other cults. The exception being the HQ, strangely enough, thanks to its layout, which enables camping behind corners and doors.

Anyway, how do you guys deal with these wretches? I must be missing something really obvious.

[Spiralize]

Full disclosure, I'm only just about to make my first attempt on Lotus HQ myself, but during my last base assault, having a scout drone (or whatever the basic AI unit armour is called) helped a lot. It actually killed two assassins all on it's own! Apparently they have some sort of innate anti-camo vision, and they spot assassins from a more manageable distance. They've since become my go-to for any mission that might contain stealth spiders as well.

[Alex_D]

The early game has no counter to it other than tactics and a methodical approach.

First, you only fight them during the day if possible. There is no reason to give them additional advantages.

Second, you use (and abuse) the smoke grenades so to "level the playing field" (the unit cannot see you either).

Third, bunch your people in an area of the map, where there are few or only one easy approach. You could lit the ground on fire so these units path their way toward your group the way you want.

Fourth and key, use scouts with motion scanners (or dogs) to step out a bit from the centre of the smoke. Once you detect a yellow arrow without a visible unit (press ALT after a scan), that's a Ninja Assassin. You can direct all of your firepower towards that location (picture Predator "Contact!" scene ).

Finally, you can speed up the research of the large HWP (aka tanks), Ninjas will attack them instead if they are closer.

[X-Man]

Research AI units as fast as you can. Scout drones can see assassins much farher than your soldiers because of thermal vision. Take a couple of drones on the mission and scout with them. But be carefull.

[TheCurse]

Research AI units as fast as you can. Scout drones can see assassins much farher than your soldiers because of thermal vision. Take a couple of drones on the mission and scout with them. But be carefull.

oh thats interesting...

well i usually just nuked the whole place with incendiary nades and (after available) heavy minigun fire, so a lot of ninjas were just collateral.
If there were like 2 left in the end and no idea where, oh that hurt... >_>

[X-Man]

If there were like 2 left in the end and no idea where, oh that hurt... >_>

Yes, in most of missions such situation comes very often, and this is the time of drones. 

[Bananas_Akimbo]

Ah yes, drones, I almost forgot about them.
I didn't even plan on researching AI any time soon this campaign. Generally I find dogs (and rats, but I haven't found any yet) to be more useful than scout drones. Guess I'll have to rethink that.

Actually I remember bringing one of those to the Lo Wo hideout mission in my last campaign. Poor thing got massacred from a blind spot. Couldn't even see the baddie. That made me not want to use basic drones any more. But now thinking about it again, I realise I did it all wrong. I should have brought more than one and covered all angles of approach. Next time I'm doing that mission, I'm gonna set up a perimeter of at least 4 scout drones and put a couple of flamethrower armed agents behind them

Also smoke, good idea. Right now I'm only using it when faced with lots of ranged enemies and I don't have any decent cover. I haven't even considered using smoke cover against melee/close range enemies. Coupled with thermal vision from drones or rats, that should really be helpful.

About motion scanners, I don't really like fiddling around with those. Indoors they are quite good but outdoors, where assassins are usually found, the short scanning range is just too bothersome for me to use. I guess coupled with smoke they're better... we'll see.

Anyway, thanks for the replies. I think I am much better prepared for Black Lotus outpost and base missions now.
My new overall strategy:
Spend the first couple of turns taking out as many enemies as possible in the usual way, so they don't bother me during my ninja-hunt later on (in my experience, ninjas tend to attack me only during the second half of a mission). Only spread out my troops enough to avoid grenades. Then lay down smoke wherever I intend to go. Apply fire liberally wherever I don't intend to go but leave a path for enemies to come to me. Guard against ninja attacks with drone reaction fire on enemy turn. Use scanners on my own turn or again, use drones for scouting.
Sounds like quite a hassle. I'll probably end up cutting some corners and paying the price

[X-Man]

Guard against ninja attacks with drone reaction fire on enemy turn.

Because they can do only an aimed shot, reaction shots with drones are unavailable.
Good tactics is to put some soldiers and 1 drone in one place, then make scouting runs with drone out for 15-20 tiles (depends of terrain type) and back to initial position (use sprint - press Ctrl while moving). Follow this for a 3-4 turns, and if there no result go find them, but move for a short distance per turn (10 tiles). OR... You can just skip for 20+ turns, and enemies will start finding you by themselves.  It is not very fun and spend a lot of readiness, but it is reliable and safe.

[Marrik]

Don't flare guns reveal them?

[Bananas_Akimbo]

Don't flare guns reveal them?

Do they? I thought the flare gun was just like an incendiary grenade but worse. I've never used it.

[ohartenstein23]

Camoflage does not work when a unit is on fire.

[Bananas_Akimbo]

Camoflage does not work when a unit is on fire.

Right, I understand. I just thought, since flare guns were specified, that they were somehow special and could maybe 'illuminate' invisible units without lighting them on fire.
Using fire on hidden assassins only makes sense, if you already have a general idea of where they might be. In which case the flare gun would be the last weapon I'd use because of its small splash radius.

[betatester]

I had good results with anti-personal mines. Especially in the black lotus HQ near the lifts. Open the lifts doors kill all what you can see. Throw mines near the doors. Let the door close. During ennemy turn wait for explosions. Repeat. Since the gear pile is near you can refill with mines.

[Solarius Scorch]

I had good results with anti-personal mines. Especially in the black lotus HQ near the lifts. Open the lifts doors kill all what you can see. Throw mines near the doors. Let the door close. During ennemy turn wait for explosions. Repeat. Since the gear pile is near you can refill with mines.

Yep, best use of mines I can think of.