Have You Played… X-COM Apocalypse

Have You Played? is an endless stream of game recommendations. One a day, every day of the year, perhaps for all time.

Everybody seems to have an opinion about Terror From The Deep, the first sequel in the original X-COM series. I’ve heard people dismissing it as a reskin or complaining that it is too difficult, while its defenders will happily gurgle about the Lovecraftian splendour of it all. The third game, X-COM Apocalypse, receives less attention than either of its predecessors but has always been a worthwhile addition to any library of games.

Apocalypse takes place in a single city rather than across the entire Geoscape of the previous games, but it’s one of the most reactive and convincingly functional worlds ever constructed for your interactive pleasure. Julian Gollop claims the original plans for the game were even more intricate than the design seen in the eventual released version. The goal was to create a future city in which every significant detail was simulated to some degree, to the extent that it would be possible to track individuals as they went about their business.

The aim was to recreate in some detail the events, organisations and personalities within a futuristic megalopolis. Each corporation had a leader who could be tailed, arrested, interrogated or assassinated. Organisations could buy and sell buildings as their financial fortunes changed. X-Com agents could spy on other organisations to gain valuable information. A sophisticated diplomacy display allowed the player to instigate aggressive or defensive alliances with other organisations. There were multiple alien dimensions, generated pseudo-randomly, and the aliens gradually expanded their empire as the game progressed.

Gollop reckoned “everything that could go wrong did go wrong” but the result is as absorbing a strategy game as I’ve ever played. I never enjoyed the real-time combat but turn-based is available, and the awe that the life of the city produces has never faded. Oh, for a Syndicate game of similar ambition. Perhaps Satellite Reign?

They don’t make ’em like this anymore but, then, they never really did.

69 Comments

  1. Fitzmogwai says:

    Yes. Actually my favourite of the X-COM bunch. Also lovely to hear a couple of references to it in the new XCOM: some of the music seems to reference the APOC soundtrack, and one of the female screams is definitely the same sample.

    • RedViv says:

      Awareness of Apocalypse makes the chatter from the Uber Ethereal in the final mission so much more creepy.

  2. mouton says:

    This was seriously the best of the old X-Coms by a long stretch. It had it’s flaws, sure, but the formula was greatly expanded and enriched. And it had interesting aliens!

    It gave one a reason to utterly destroy some maps. “Welcome, travelers, to Cult of Sirius Enrichment Center, have you come to OH SHIT THEY ARE BURNING EVERYTHINAAARGH”

    • Moraven says:

      That is what I liked the most. You could blow a building up from your vehicles or take a mission and drop incendiary rounds all over the place.

  3. Skodric says:

    A true classic. Still playing it to this day (although it can be a bit of a faff getting it going). The ability to literally raze buildings to the ground by the judicious use of overwhelming firepower never gets old :)

  4. jalf says:

    I always felt it fell short. There were a lot of really good ideas in it, but it never really came together, I guess. I would have loved to see the game he originally intended it to be, though.

    It was definitely an interesting game, and I’m glad to have played it. But it just wasn’t anywhere near as tight and cohesive an experience as the first X-COM.

    • jezcentral says:

      Agreed. There were so many systems that they didn’t gel properly. More gameplay testing would have helped, I think.(I never came across a bug, though, so the rest of their testing seemed to be okay.

      But, yeah, don’t play it turn-based. It really doesn’t work. Real time it’s the way to go.

      • mouton says:

        No idea what you are talking about. Finished it turn-based, it played pretty much like the earlier x-coms. Only used real-time to hasten some mop-up operations.

        • Press X to Gary Busey says:

          It was only really balanced for the real-time mode. It’s almost broken in turn-based with the free roaming brainsuckers, hyperworms and poppers. The excruciating civilian turn… (dual wielding toxiguns is god mode in both though, but still in line with the other games getting easy with molecular and mind control).

          It’s very fiddly and has a lot of micromanagement before you get a hang of all the soldier settings and hotkeys. Perhaps it was just ahead of its time trying those things. The UFO After-Trilogy reused some ideas and made pausable real-time somewhat easier to handle.

          • mouton says:

            It’s very fiddly and has a lot of micromanagement before you get a hang of all the soldier settings and hotkeys.

            Fiddly and a lot of micromanagement? That sure sounds like the first two games alright! Ah, the inventory tetris…

          • Asurmen says:

            Dual wielding in turn based doesn’t give you any benefit but you lose out on cloaking.

  5. mattevansc3 says:

    Apocalypse was a weird game. Its my favourite X-COM by a country mile yet it was the one I was most disappointed in.

    The alien types were inventive, the weapons had a good variety, the destruction was brilliant. Sod the “blow a hole in the wall” tactic from Enemy Unknown just chuck a landmine at a pillar and watch the entire floor come crashing down. And seeing a mothership warp in for the first time creates a level of dread that no other X-COM (or XCOM) game could ever achieve.

    When you play it you can see the groundworks for a classic, genre defining game and you just feel almost “cheated” that it doesn’t. Also Toxin C just kills the game out right.

    I just wish we had an X-COM Apocalypse 2 that fulfilled the potential of this one.

    • Artist says:

      Oh, that would have been wonderful. Im still sad that XCOM didnt continue where Apoc left off. Maybe an unfinished jewel, but a true gem nontheless!

      • mouton says:

        Firaxis might follow through in that direction, at least in terms of futuristic setting. With the success EU has been, it is plausible that they will make some kind of a sequel and I think they ruled out “terror from the deep”.

        • mattevansc3 says:

          The problem is that XCOM went in the complete opposite direction to Apocalypse.

          Apocalypse’s major improvements were in the geoscape. In its presentation, in the UFO combat, in its time nature, the potential for politics, etc. XCOM took the geoscape and threw it in the bin.

          • mouton says:

            Yeah, yeah, we all know how some people are bitter for EU not being whatever they imagined it would be, but I am talking about a possible future game. Contrary to what some might think, Firaxis’ mission statement is not “crushing dreams”. They just might, you know, improve things that were flawed! But, that never happens.

          • Stellar Duck says:

            mouton, I appreciate what you’re saying and XCOM wasn’t bad at all but it was a very, very different game from X-Com Apocalypse. I’d like Firaxis to make another but I hold no faith it will be anything like Apocalypse. That’s simply not how they make games. For good or ill, a Firaxis game is smooth as hell (aside from the pervasive bugs on launch and a penchant for only getting good with the expansion) and Apocalypse wasn’t a smooth game at all.

            It was a sprawling mess where you could do as you pleased. Raid the Cult of Sirius time and again? Sure thing! Make money by making psi clones and selling them to Diablo? Sure thing! Raid said drugs from Orion and sell them? Sure thing? Oh, and I guess I should deal with the alien menace as well.

            XCOM is good, but it’s not Apocalypse good.

          • SpoonySeeker says:

            Mouton, Firaxis’s mission statement is delivering stable games on time, regardless of how many features have to be cut. That is why Sid Meier is beloved by publishers and he runs his company the same way.

            Sure, Firaxis makes decent games. But they are NOT the developers you want making a sprawling feature-rich game like a potential Apocalypse sequel.

          • mouton says:

            @Stellar Duck

            I don’t know, Firaxis games can also allow for doing as you like. Civ games, despite their flaws, are very open – so open, actually, that they are a joke in terms of any kind of historicity and for that I go to Paradox games and such.

            @SpoonySeeker

            I had tons of fun with EU, despite its considerable shortcomings just as I had tons of fun with XCOM/TfD/Apoc, despite their considerable shortcomings. As written in this article, Apoc had an insane number of features cut despite being developed by Gollop. And even if all goes right, cutting content is an inevitable part of a development process.

            Either way if a Firaxis sequel comes out, it will be judged when it arrives. I simply have – personally – no reason to be overly pessimistic.

          • Stellar Duck says:

            I like Firaxis. SMAC is perhaps my favourite game of all time.

            Civ 5 is decent to goodish. Enemy Unknown is pretty entertaining.

            That said, they’ve never made any games that were even close to the openness of Apocalypse. That’s simply not how they do things. That’s not a criticism, that’s just an observation.

            Civ 5 is somewhat open, yes, but it’s only open within a rather narrow scope. Civics are gone for instance and that limits its flexibility and openness a great deal. When you choose a civic you’re locked into it for all time.

            I’ll quote Serrit down below:

            “I remember falling out with Transtellar due to collateral damage during a UFO invasion, which meant my future hires could no longer travel to my base by taxi (damn your monopoly Transtellar!).”

            That’s something that’ll never happen in a Firaxis game. At all. The sheer nonsense of the situation is outside the scope of their designs. They’re, for better or worse, very stream lined and directed experiences. That’s fine. It’s just also very, very different from what Apocalypse was.¨

            Edit: I have no doubt that a new Firaxis XCOM game would be good. It just won’t be the same design philosophy as the one behind Apocalypse.

          • socrate says:

            What people don’t seem to understand is that before gamer wanted smart and complexe gameplay while also making it interesting…today gamer are more numerous in casual gamer that don’t really want to put the effort in playing a game,you end up with game like skyrim that make you kill a dragon in 10 min of gameplay…in xcom enemy unknown you only have to use that dumb auto reactive shot aka overwatch and you will never have any kind of loss if you go slow…its silly and remove everything that was xcom which is tactic…but gamer today are like that…they want badly made and easy game cause they don’t want to really put their mind at it and don’t care if a game is well made or not since they will go back playing call of duty the next day and not care about this game ever again.

            Its what publisher do…they are there to maximize their profit and have no care about customer just look at civ 5 which had tons of removed stuff that had to be fixed by patch and expansion and even then the AI still wasn’t that great and the game still had tons of downgrade compared to civ 4…really thats why people love and have hope in kickstarter i think and are tired of publisher who care only about profit instead of making game you will play 10 year later and will have good memory about.

            Also im not sure if you remember these game really well terror of the deep was awesome for the underwater feeling but the game was massivly broken in tons of unfun way so was apocalypse which i just retried to be sure and the game really is not meant to be played in turn based combat and as other really bad flaws and was obviously rushed with tons of content not being introduced or maybe just horrible design decision.

            That said xenonauts was a really fun(it didn’t really improved alots of xcom thing that needed it but still)experience compared to the new xcom which didn’t even have good environement impact but was more of a homage then an improvement,but is still a game that is a million time better since it push the player to actually play strategicly which is why xcom was so unique…so try it if you haven’t its not godlike but its quite good.

          • Kaeoschassis says:

            @socrate: It’s pretty funny* how you’re trying to frame this as new information that people “don’t seem to understand” when infact it’s the same stereotype that’s been thrown around for years upon years.
            There are gamers of every type. There are games of every type. This has been true for a very long time and will continue to be true.

            *No, it’s not.

          • Raoul Duke says:

            Exactly. XCOM basically took most of what made X-COM interesting and threw it away. It’s actually pretty much 100% linear, which is very, very disappointing.

    • FlatBat says:

      Personal favourite (apart from the first mothership) was being able to teleport next to an alien, steal all its stuff, leave it with a primed hand grenade and teleport out.

  6. JonasKyratzes says:

    I loved X-Com: Apocalypse. It was one of the first two PC games I bought myself. Replayed it a couple of years ago, and it’s still excellent.

  7. zapatapon says:

    The game was brilliant overall but I always felt the aliens looked positively ridiculous. I suppose a deliberately cheesy B-movie aesthetic was aimed for but for me it made the adversary difficult to take seriously.

    • mattevansc3 says:

      The aliens looked terrible? The UFOs looks like oranges!

    • mouton says:

      In Apocalypse? As opposed to the first game? With Mutons in green pyjamas? Or that frutti-di-mare stuff in Terror from the deep?

      • Baffle Mint says:

        I was never able to get into Apocalypse for the incredibly shallow reason that the alien designs in it really, really bore me.

        Silly as the art in the original game is, at least the different aliens are distinct from each other and memorable looking.

        All of the Apocalypse aliens look like tumors removed from a Headcrab. And that’s not even an awful look, it’s just that they ALL look like that. Part of what I loved about the original game was discovering what kind of crazy new alien I’d be fighting next, and you don’t really get that as much in Apocalypse, because the answer is always Headcrab tumors.

        Also, I have never forgiven the original game for making Silicoids and Celatids just blobs. I studiously avoided looking up what the aliens looked like when I first played the game, and I was really exited to see what the later terror units are, only to have them be just big wads.

        • FireStorm1010 says:

          :) I think when you do the autopsies, thew screenshots of the aliens are pretty good , but i admit the miniatures 3-di ngame look often weird.

          I remember reading somwhere Gollop or someone involved in the game saying it was a case of part of the art being done by different team or even company…

          • rmsgrey says:

            Yeah, I heard that the third party artists produced these absolutely gorgeous high-detail high-resolution models, that looked great when they were allowed to take up most of the screen, but looked like blobs of plasticine when reduced down to in-game size…

      • zapatapon says:

        I can only echo what Baffle Mint said. XCOM’s aliens are silly , Apocalypse’s are ridiculous (and yes, also their ships).

      • Raoul Duke says:

        Pretty sure the original X-COM has a resolution of 320×200 (!) so you can hardly blame them for having unsubtle colour schemes.

        Funnily enough I have the same ‘samey’ complaint about the new game. All of the aliens are sort of extras from Quake 2, brownish tough things with machine bits tacked onto them. It lacks that sort of naive X-Files charm that the simple grey aliens from the original game had.

    • Press X to Gary Busey says:

      One company did coding and game design (Mythos) while another company (MicroProse, their publisher) had a team doing the artwork. The strange art style choices are from lacking coordination between the two plus some failed experiments from the art team just doing whatever they wanted.

  8. manio22 says:

    I second that. For me was the best x-com . The choices you made had an effect in the game. If you didn’t protect Marsec for example, they would turn unfriendly towards you , meaning funding stopped and you couldn’t buy new vehicles from them . Also you could literally level the whole city! Baaam! What wouldn’t i give to see all the stuff devs wanted to implement. Yet they made 180 turn and create Interceptor…go figure.

    • Artist says:

      Theres no “they” past Apoc! Gollop and his brother have only been involved in X-com and Apoc. From that on it was just cannibalizing a well-known franchise! Well, can be discussed if XCOM is reinvention or further cannibalization…!

  9. mashkeyboardgetusername says:

    Yes I did! Absolutely loved it. Add my name to the “favourite xcom game” list. And they way I usually ended up playing it (once I’d accidentally winged a few buildings and everyone hated me so I might as well raid them anyway) it’s also may favourite “rouge PMC” game.

    I just loved how alive the city felt, with all the systems churning away in the background. If the transport network was damaged people and equipment couldn’t move. Corporation attitudes affected what was available and for how much. Aliens were actually in the buildings they beamed down to and then spread out. If an alien escaped your raid on a building it was probably in the building next door. And so on. Terrific. Also massed pink laser battles. Those were brilliant. Sorry, gushing with nostalgia here.

    Never actually finished it though. Always got the the stage where the aliens couldn’t really attack any more and then felt that I’d won. Ho hum.

    If only I knew where my disk was, and the Steam version didn’t occasionally ask for the CD…

  10. Ben Barrett says:

    There’s a seriously good set of LPs of the various XCOM games that have come out of Something Awful over the years. The Apocalypse one is arguably the best with some pretty incredible meta-storyline stuff crammed on top: link to lparchive.org

    • AXAXAXAS MLO II: MLO HARDER says:

      Just when I was thinking “This game is interesting but I know literally nothing about it other than these few paragraphs” you come in to save me. Thanks, Ben!

  11. supermini says:

    Yes, and I loved it. I replayed it about 2 years ago and it holds up well apart from some interface niggles.

    The real time combat is quite good, actually, I preferred it to the time units system. It kinda falls apart when you get personal shields and type B toxin (that gets through shields). Combat difficulty just takes a nose-dive at that point.

  12. Serrit says:

    I fell in love with X-Com Apoc after reading Chris Anderson’s hints guide that was given away with a PC Zone mag (even though the game did take ages to load tactical missions on my Pentium 75Mhz).
    I remember falling out with Transtellar due to collateral damage during a UFO invasion, which meant my future hires could no longer travel to my base by taxi (damn your monopoly Transtellar!). I would have been fine with my hires taking the slower people-tubes, but the aforementioned collateral damage had also destroyed some key routes, meaning they couldn’t get to my base for a few days until the city had repaired them (which corp was responsible for municipal matters?)

    Being short on funds to offer a settlement to Transtellar, I tried a campaign of violent raids against their operations in an attempt to get them to come to me begging for a neutrality agreement. Sadly they were more than happy to remain being grumpy with me, and my lack of focus on the aliens led to Mega Primus’ (and X-Com’s) downfall. Ah well!

    • Stellar Duck says:

      “I remember falling out with Transtellar due to collateral damage during a UFO invasion, which meant my future hires could no longer travel to my base by taxi (damn your monopoly Transtellar!).”

      And that’s why this is the best X-Com game ever made, XCOM be damned. A good good game indeed but so shallow!

  13. NotToBeLiked says:

    My favourite X-Com game ever. Having to deal with the companies to keep your supplies up felt way more sensible than the whole contrived has withdrawn its funding for you fighting a WORLDWIDE ALIEN INVASION because they get attacked by aliens… I loved the fact that you could just go on a raid to any company and destroy their buildings, even if there were no aliens there. I’d love a modern remake of that, instead of the latest “My First Turnbased Game”-XCOM. I was 12 when I played Apocalypse, I could barely understand English and I still managed to figure it out. I’m quite sure gamers of today can figure out an XCOM game that had some complexity to it…
    The part where you invade back was pretty dumb though…

  14. Lord Custard Smingleigh says:

    On one playthrough I managed to capture one of the charging kamikaze exploding aliens alive, and that research bounty unlocked the indescribably powerful Toxin-C ammunition, which made every other weapon in the game obsolete.

    Also: The autopsy picture for the building-sized city-leveling Overspawn has wrecked police cars inextricably mangled into its torn body.

    • mashkeyboardgetusername says:

      I know Toxin C was amazing (kills stuff and ignores shields) but I still stuck with the pink lasers because, well, look at this: link to warosu.org
      Isn’t that magnificent?

      • Ben Barrett says:

        what the shit

      • geldonyetich says:

        That’s a pretty good way to get all the corporations in the game to hate you, considering they really don’t like their buildings getting damaged very much. That’s the main benefit of Toxin-C. That, and it pierces shields. (Although, when it comes to the Cult of Sirius, the more property damage the better)

        • mouton says:

          AHAHAH INCENDIARY AMMO AHAHAHAHAHA

          • sinister agent says:

            A level where there are only one or two stairways from the top of the building, where the guards sometimes started, and which by chance, I happened to take out very early into a fight.

            I spent probably the better part of an hour laboriously carving away the entire foundations of that building, and the feeling when the last wall broke and the whole structured collapsed in a shower of floor tiles, tables, and bewildered guards was glorious.

  15. Tom De Roeck says:

    Definitely my favourite of the X-COM series. Had a good concept for a game that was similar, but not fighting aliens, just gangs or similar. note: Ive never played syndicate.

    • Raoul Duke says:

      Syndicate is brilliant (well… Syndicate WARS is brilliant) but it has basically none of that organisational level stuff in it at all.

  16. philosoma says:

    Apocalypse is the best! Playing Xenonauts felt a bit lacking and basic afterwards. Defiantly prefer the semi real time mode more. /me goes to find my Steam copy…

  17. Premium User Badge

    Bluerps says:

    I played it when it was new, but bounced off of it then. I think it was just too different from what I expected from an XCOM game, both visually and how it worked.

    I warmed to it much later, when it was already old enough that it was only possible to play it via Dosbox. It’s still not my favorite XCOM – and I don’t think I’ll ever really like the weird ‘flying cars and rocket ships’ design of the XCOM crafts – but I enjoyed it a lot and I think it has a lot of interesting ideas.

  18. mutanteggs says:

    I’ve been trying to get into it but i just bounce right off, too complicated for me.
    Any sort of hints or something?

    • mattevansc3 says:

      Which bit is complicated to you? If you want a beginner’s strategy buy nothing but flying motorcycles until you get the researchable craft. The standard craft are all to weak to take on the UFOs but the sheer numbers of the motorbikes can take down a mothership.

    • Press X to Gary Busey says:

      I bounced off it when it was new despite loving the first two games. It’s very unforgiving just throwing UFO’s at you right at the start and a lack of in-game help.

      I played it through a few years ago after watching some episodes from this link to youtube.com He does a good job explaining the game to new players.
      That one is in turn-based but he did a second playthrough in real-time.

    • Raoul Duke says:

      Same – I am completely obsessed with the original UFO/X-COM but found Apocalypse bewildering in the extreme due to the overly fiddly interface and lack of any kind of in game explanation for… anything.

  19. slerbal says:

    I love this game so much. They might not have achieved everything they set out to, but the world felt convincingly real and the corporations were a very tangible foe/ally.

  20. Blue_Lemming says:

    Didn’t love it overall thanks to the half turn based combat system, and some of the aliens were just blobs, BLOBS i tell you. Then again when you put it up against all the other xcom games, it does ok.

  21. Josh W says:

    Oh yeah this game, played it with one of my housemates in uni for hours/days. We happened upon the non-lethal raiding bug by accident, and decided to raid the local gangs and the cult of sirius into the dust. Can’t remember to what extent stealing all their stuff actually impaired their operations, but it seemed an amusing way to cheat ourselves to more money and experience, in what was otherwise a very demanding game.

    I always wished when playing it that we could have randomised city layouts (but with different working layers of infrastructure), randomised starting influence of different factions, what I now think of as Gal Civ style politics.

    • sinister agent says:

      There actually was a big random factor to most of the corporate relations at the start. I’ve read accounts of people who started in a situation that somehow ended up with the Cult of Sirius allying with Megapol, who obviously got pissy with the player for attacking the Cult. The big alliances/antipathies were more predictable though

  22. sinister agent says:

    Yay, Apocalypse! Easily my favourite of the series, and I always played it in real-time mode, too. Crazy, I know.

    You can see a lot of the unfinished bits once you’ve played it through a few times and read all the flavour text. Or even just played enough of it to realise that, for example, all the ground vehicles are utterly useless. A real shame. But none of it’s broken and what is there is so much fun, so full of character and imagination – it also features the best aliens of the whole series in my view, especially once you find out what’s behind the invasion.

    Some great music, too. Very spooky and dramatic. A shame it was a bit of a dead end really – Abomination was a distant cousin I have a real soft spot for, but was flawed all over the place. The UFO After-whatever games obviously took a little from Apoc as well, though not nearly enough. Fantastic game.

  23. Premium User Badge

    Ninja Dodo says:

    The demo of this game (from a PC Gamer CD) destroyed my newly bought PC in 97. Crashed and wiped. Thankfully still had warranty on the thing but I never attempted to play this again. I suspect my taste in games might have turned out different if this had been a formative game. New XCOM convinced me I can definitely enjoy turn-based strategy so I guess I’ve been missing out.

  24. SurprisedMan says:

    Those Jammy Dodgers look a bit off to me.

  25. FireStorm1010 says:

    Loved it. It was an abosolutely great game of enourmous scope , with maybe a bit strange aesthetics, which had its charm tough/

    One of the things imho that it made best out of all Xcom games (including my beloved XCOM EU) is air combat. Seeign and comanding your ships converging on the ufo, destroying the city below, was absolutely amazing.

  26. Timberwolf says:

    My favourite X-COM by far. I don’t think I’ve seen another strategy game do destructible terrain so well – I remember one particular battle in slums with a hostile organisation, lobbing rockets up at some gang members on a balcony and tearing open the apartments behind them.

  27. rmsgrey says:

    I have fond memories of spending an entire afternoon with disrupter(?) rifles (infinite ammo guns that run on beamed power from the alien dimension) systematically chipping my way through the support pillars of a large building owned by a hostile corporation in order to pulp the aliens lurking within without exposing myself to the inevitable ambush a frontal assault would entail…

    Later in the game, on a raid into the alien home dimension, my heavily-shielded Avenger got cut off from the portal by the mass of UFOs – so it embarked on a hit-and-run war of attrition – wandering in just close enough to attract a UFO’s attention, dealing damage, then retreating to the fringes to recharge shields. That one raid ended up wiping out the entire alien armada, and then a follow-up took out their craft construction capability, leaving them impotent as my forces rolled up their remaining structures and eliminated them.

    While I enjoy Enemy Unknown (even more with Enemy Within), it is very much a designed sequence of events with every experience planned and tested, with none of the emergence-from-simulation that graced the classic XCOM games. An example from UFO: alien bases – in that game, the aliens send craft to scout possible base sites, send UFOs to prepare the area, and finally send a couple of supply ships and a battleship to install the base, then send a supply ship every couple of weeks or so to keep the base supplied. Depending on your interception capability, you can disrupt the process by shooting down the scouts, take out the battleship and supply ships when they come to install the base, or raid the base once it’s in place. Or you can leave the base in place and farm the supply ships as a reliable supply of alien technology (particularly elerium). In Enemy Unknown, there is only ever one Alien Base, which is a special story mission, that you need to do in order to advance the plot, and the only side effects of its presence or destruction are the new reasearch options and the game progress unlocking new aliens – no in-game logic to it, just a magic trigger for game design purposes…