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Was not able to fully infiltrate but close enough (90ish percent) that a 4 man squad could complete the mission taking out 15 aliens and getting enough trooper corpses for instant autopsy research on them. Definitely seems like it's worth it so far. Will have to see as the game progresses.
I built a lab as my 2nd facilty so I could put my 2nd scientist to work there and get my research progress back on track.
Supply raids are hard to detect, especially early game. Troop column ambushes are not, and once the region is strength 4 you can find those. That's where I get most of my corpses. Soldier advisors also detect faceless, and you get corpses from those missions too.
I also prefer to have soldiers as advisors for the inevitable retaliation missions; they go much better with that extra soldier. Having a scientist out there is a liability.
Having a network tower in the region boosts your scanning detection, as does having the avenger in the region.
In my current campaign it's early in the 3rd month and I already have 6 engineers, 6 scientists and enough intel that I can use it to boost infiltration fairly frequently when I see a good mission that has a questionable timer. I only actually paid for 1 engineer and 1 scientist. The rest came from missions.
3 months isn't really long enough to tell for sure of course. I might just have gotten lucky in my current campaign, but I'm definitely seeing a much higher frequency of missions detected. So I can focus on doing the best ones and ignoring the other ones.
I did train up a few specialists specifically for haven duty giving them both scanning protocol and a battle scanner so I can rotate them around my havens to root out any faceless. I put whichever havens have the most rebels on intel with a scientist adviser and the rest on recruit with scanning protocol/battle scanner specialists as advisers.
The other issue I was running into sometimes without the scientists with low rebel count havens is that I would sometimes just not find anything usable at all for weeks at a time. Slower research is annoying, but having my soldiers sitting around doing nothing for 3 weeks is worse IMO.
Scientist advisers frequently give me missions that have a timer of more than 10 days and almost always more than 5. I also find some of those harder to get missions like UFO landings and supply convoy raids with a timer of more than 3 days so I can actually do it.
I'm not using any scientists as advisers right now but all of my havens are maxed out at 13 or more so they all produce missions with good timers without the scientists.
But if you don't get early scientist rescues and have to buy all those from BM, you hardly can spare it. Otherwise the advent force will outpace your research too much and you'll have a painful midgame transition (around magnetics timer).
And generally I will have one liberated region with an engineer, and the other regions all having about 6-7 rebels on intel. This does the trick for detecting missions, as having any more rebels on intel or scientists for that matter doesn't really contribute to detection after that.
I do still put my first scientist on haven duty until I have my first 3 missions in progress because I want the best chance I can get for getting decent timers when all I have is squaddies and rookies. After that I swap them out for soldier advisers now.
I've accepted that there are times where I will have zero missions running because I haven't found anything with a timer longer than 3 days in awhile. It's more important to focus my intel on the regions with the lowest strength until I've got at least 2 or 3 full teams of high rank soldiers with mag or better weapons. I usually do still have at least 2 or 3 squads on missions most of the time even in the first few months.
I don't want to get stuck doing retaliation missions with a bunch of lance corporals with conventional weapons and kevlar armor. I also don't want missions with higher level enemies due to high advent strength level.
In the first few months I want relatively easy missions that I can use to level my first 3 squads up to staff sergeant or higher. Then I can start doing some harder missions when I have troops that can reliably kick some ass.
I'm actually starting to think psi ops might make the best haven advisers since they're better at rooting out faceless. And since I usually do a psi rush, I always have way more psi ops than I do of any other troop type.
I still use technicals as advisors because they're just better at dealing with faceless rendezvous missions that almost any other class, at low levels too. Their flamers can make a mess of a pod if they manage to get the first action in (especially with napalm-x), and their rocket is an "oops" button incase things don't go your way.
I almost never lost any rebels when using technicals on those missions.
I really only build RLabs if I low roll scientist rescue missions and am tied to only 1 scientist purchase per month from black market on commander, and I frequently make one a haven adviser, generally for a short term, in the main area where I want to do missions.
If you have to skip mission cycles due to poor intel, research being ahead still won't cut it because you'll be behind on level and lack the aim and skills to deal with rough situation. Good intel also means more intel to spare to boost mission timers to snag a short one in.
And well promoted psi ops generally let you succeed at missions while behind on tech for quite some time. I typically only start panicking about tech if I encounter my first sectopods with mag weapons.
I tend to like the Psi rush because they start with soulfire right from the start which is basically the equivalent of a cannon that never misses and then they continue getting additional options that are guaranteed as they level up like null lance, stasis, etc. So as you said, they help carry my teams through the early part of the game while I'm still scrambling to get laser weapons researched and built and nobody has good enough aim to consistently hit everything.
Since I almost always do a Psi rush it means I'm almost always low on scientists unless I get very lucky on mission rewards. I want 6 scientists asap so I can have 2 in the psi lab speeding up upgrades on my psi ops and 4 in my lab doing research. I usually train my first psi op sometime in April.
I don't usually play legendary. I like commander with A Better Advent. Gives me tougher enemies than usual for LWOTC without such a huge time and cost penalty for everything.
I believe Psi ops have the same chance to detect faceless as a specialist with scanning protocol and then both of them also benefit from a battle scanner if they have one. I consider scanning protocol kind of a waste of ability points since I almost never use it on missions. So it's only real use for me would be haven adviser duty, and I pretty much have a specialist on every mission so I don't have extra specialists to spare for haven duty like I do with psi ops.
My secondary options for haven duty are usually either technicals or grenadiers. Technicals are a bit questionable to me since faceless missions yield corpses so I never want to use a rocket or a flame thrower if there's even the slightest chance of destroying a corpse. So a grenadier with needle grenades works better for that IMO. Once I get mag weapons then it's not as important since some of my rebels will then get laser weapons instead of conventional.
So I worked on psi lab rush / laser skip into fast magnetic for several runs until my first cmdr win with that opener. What slowly changed in my playthroughs was to
1. stop buying the psi lab upgrade
2. trying to avoid assigning scientists to the psi labs as much as possible
I just try to avoid picking an end game skill that takes forever to train too early on the psi ops but ultimately, even if they are awaiting a promo and go on a mission, they still earn exp. I think they minimally need to do 1 mission after a promo to level up again but I'm almost positive that the exp earned between contributes to the next level. Like, despite that slow early promoting, I still had 4 MSGT psi ops before I had 4 MSGT of any other class in my one win game.
The struggle with that opener is in the last few weeks before magnetics unlock where you still have basic weapons and start to encounter stronger enemies as you pointed out. This is the only point in the game I occasionally skip missions or an entire mission cycle to avoid major injuries/deaths but it's still generally possible to do 7-9 missions with 5-6 units if you bring 1-2 psi ops on them (excellent or flawless).
For much of my learning playthroughs until my first win, I would tend to have fairly rigid class builds because it's easier to mishmash a viable comp this way. And in that setup, all of my specialists were strictly healing bot(top row) officers so I would only have scanning protocol if I played with the option to buy skills with xcom ap. But I would never have put a healing officer as a haven adviser (or at least never have done the faceless mission with such a ♥♥♥♥♥♥ shooter). I played with Commander's Choice mod so it was easy to have all very low aim specialists.
In more recent playthroughs I'm trying to flex setup a bit more with like stealth shinobi officer, technical officer, grenadier officer, holo bot officer which leaves more creative build space for other classes. A decent base aim overwatch specialist is a pretty decent unit for scanning protocol and scanning protocol is insanely valuable on missions. At least if you play without reloads of any sort it can save your ass on shinobi reveals or spare you a double pull on an already hard pull.
Basically, if I play with the option to buy extra skills with xcom AP, 100% of my specialist get scanning protocol because it's that useful as a free action. It's just that this tier is otherwise extremely build defining for the class and so scanning protocol is always 2nd best pick for the healer and hacker builds.
So one of the nice things about psi ops is training them up from a rookie takes significantly less time than training any other class in the GTS. So you can quickly ramp up to a decent number of psi ops once you get the psi lab. I only put scientists in the psi lab when I have 2 psi ops in training. If I only have 1 then I just let them train without a scientist helping.
I tend to prioritize fuse on my psi ops since it's a free attack. So the combination of soulfire and fuse on most of my early psi ops gives me a very effective means of guaranteed damage until I ramp up to laser weapons. I don't skip laser to go straight to mag because both are required if you want your rebels to have a chance for their weapons to be upgraded. Also mag requires elerium to build and lasers don't. Early on I am VERY low on elerium and on commander or higher I really can't afford to spend supplies on elerium in the black market.
Also to me the first 2 months is really devoted to getting my base set up. I spend almost all of my supplies initially building a GTS so I can buy wet work and vulture, then building a Psi lab, a Lab, a workshop, and a power relay. By May I usually have my base done except for the shadow chamber, defense matrix, and infirmary. That's when I really start pouring supplies into weapon upgrades. So early May is rough for me usually, but by late May I've got lasers for everyone and am working on Mag.
May is usually also the month where I start the ball rolling on proving grounds projects. So I'm getting both weapon upgrades and proving grounds upgrades starting in May.
I use commander's choice as well because of the built in "not created equal" component of LWOTC. I also pretty much always take the 2nd wave option to allow buying extra skills in the training center. So initially my specialists all get combat protocol and trojan to deal with robotic enemies and then after I build the training center they also get healing protocol. All specialists get field surgeon, that's just a no brainer for me. Most of my troops end up pretty cookie cutter unless I get a combination of xcom row perks that makes different choices more viable. Drones are actually surprisingly annoying on commander or higher. It's not uncommon for me to need 3 attacks to kill 1 drone if I don't have a specialist. A specialist can 1 shot it guaranteed.
I've tried overwatch specialists, but I'm not a fan of relying on the RNG so much and hoping that my units randomly kill stuff when it's not my turn. I usually only use overwatch when I just don't have any good shots. If my choice is between a 25% shot or going on overwatch I'll pick overwatch. I usually make most of my officers shinobis since in the majority of missions, my shinobis remain concealed for the first 2 pods for scouting. Being an officer allows them to contribute offensively without revealing themselves.
If I really want to rely on overwatch I find sparks a better option personally, but I don't tend to build them most of the time since they're generally eclipsed in power by regular troops later on. They do start off stronger than regular troops though.
I could see getting scanning protocol if you don't use stealth scouts but I almost always have a stealth scout on every team whether that's a shinobi or a reaper. So Scanning Protocol is only of any real use to reveal the Assassin. Not a good enough reason to take it IMO. The psi op perk that helps for revealing faceless is one they get automatically when you first train them. So there's no tradeoff there, and they get it sooner than the equivalent specialist perk. Now if scanning protocol remained in effect for the rest of the mission after activating, or maybe for 2 or 3 turns after activation then I'd be more likely to take it.