Having read the proposed story lines, and having found major issues with all of them (chiefly in terms of the mothership, but I have to admit that all of them have major logic gaps), I have an alternative to propose.
First of all, my assumptions, based on in-game details:
1. The aliens, while generally more advanced than we are, are still only one or two centuries ahead of humanity (probably closer to one century ahead, or less). This is born out by both the sheer variety of concepts that the aliens appear to copy off of human designs, such as variable hard points, and by the fact that most alien technology can be unravelled and used by humans. It is also probably something that can be inferred from the simple fact that the aliens did not simply take a few monkeys or whatever, and then just dump a crapload of class four pathogens to include us all in the XVI hive mind.
2. The aliens are not actually a single hive-mind, but many hive-minds--probably at least one per solar system, if not actually one per planet. In short, there is no mother-ship. There is no single target that will eliminate the alien menace for all time. In point of fact, there is no one target that humanity can take out, and thus leave the entirety of the alien tech-base functional and just waiting for us or somebody else to swoop in and pick it up. What this means is that if humanity is to win the war, we must scare the alien hive-minds. We must prove to them that we can hurt them as they have never been hurt before.
On a story note, I have to admit that I feel that this was one of the X-COM games' major weaknesses--that the aliens, despite hugely advanced technology, were still extremely vulnerable to a decapitating strike. If we are looking at any kind of true hive-mind, that is simply unlikely to be true. This view is supported in UFO:AI by the simple fact that the aliens do not become sentient until there are a certain number in close proximity...and once they become sentient, they do not become able to instantly transmit data to every UFO in the system. Clearly, there is a limited range of telepathy, which means that telepathy across inter-stellar distances is improbable.
3. The aliens want humanity to join their hive-mind. My own favorite reason for this, by the way, is the sugar-protein combination theory. Basically, there are two possible combinations of atoms for every sugar or amino acid molecule in existence, and they are mirror-images of each other. Because of the way they interact, the reality is that a race such as humans, who have a left-left combination of proteins and sugars, can only colonize 1/4 of the available planets in the galaxy.
The aliens, as seen so far, have three races. Ah-ha, I see you saying--that means that one out of every four habitable planets the aliens find, they cannot use. So, the aliens, knowing as they do that they are the only truly advanced race in the galactic neighborhood, go looking for a race that does have that particular sugar and protein combination. Humans are it.
Ok, on to the story, as I see it.
About 300-500 years before UFO:AI begins, one of the various nations, corporations, or whatever on the Taman homeworld develops a biological equivalent of the internet: a virus-like organism that forms a symbiotic bond with its host, allowing said host to share every thought, memory, and so on. Now, the Taman, it must be understood, had never been cursed (blessed?) with any kind of world-spanning conflict just as electrical energy began to emerge as a wide-spread energy source. Nor was there any kind of long-term conflict between two super-powers like the United States and the USSR. Because of this lack, the Taman had never truly felt a need to develop electronic devices for the purpose of high-speed calculations. Remember that--it's important.
Anyway, about 200 years before the start of UFO:AI, a Taman research outfit managed to create an organism that would like two or more minds together to enable them to act as a single entity. Whether this was done to prove that it was possible, or done as a rather cold-blooded attempt to make research faster, cheaper, and easier, is irrelevant--by performing this experiment, the Taman accidentally created their first actual computer. On Earth, computers absolutely transformed science in every respect. Perhaps not unexpectedly, they had the same effect on the Taman homeworld. Companies and nations which were willing to sacrifice a few dozen (or more) citizens or employees to transform them into into these hive-mind computers had a major advantage. Companies and nations which were not, didn't. They spread like wildfire, and, as on Earth, it was not long before people were volunteering to become part of these psionic networks. Within twenty-five years of the first discovery, the aliens had their own version of the world-wide web, one powered not by networks of computers, but by the actual brains of sentient beings.
It honestly didn't take long before an entire generation started being born in places that had no notion of what it was like to not be part of this network--to be part of a communal network of entities from birth. This new generation had no real concept of individuality--just like on Earth, the networks brought this new generation closer together than ever before, but unlike on Earth, the connection went much deeper, and was much more a part of each new Taman that humans could ever achieve. Within seventy-five years, the Taman who remembered what it was like to be individuals began to die. Within a hundred, the only Taman left had always been part of the group-mind, and could not imagine existing without it. There were no poor regions of the Taman planet to impede this progress--the Taman had avoided the world wars we suffered through by the simple expedient of ensuring that all regions of the Taman homeworld had what they needed to grow from the earliest possibility. By the time the last of the original creators died, the entire Taman home world was a single entity.
Guess what? It got lonely. The eight billion Taman that were part of it might not think of themselves as individuals, and might not be individuals, but they still had the same psychological needs as individuals. They needed somebody to talk to.
So it set out to create a new hive-mind, someplace far enough away that the old hive-mind would not simply assimilate it from the beginning. A space program was developed, relying not on electrons for control, but on actual hands and fingers on (often) mechanical buttons. Probes were sent out, new worlds found, and finally one that could support them was found. The Taman colonized it, and life was good. But then both hive-minds got lonely...and so they decided to repeat the process. It went faster this time, both from the previous experience, and because there were now two worlds to draw upon.
By the time the Taman encountered the Orkinoids, which I would judge to be about seventy-five years ago, any thought that any race might not welcome them with open arms was long since gone. The Taman, who by now had nearly a dozen worlds, landed, attempted to introduce the Orkinoids to teh XVI micro-organisms, and watched in horror as the orkinoids died slowly and painfully. The orkonids, of course, reacted accordingly. Although still not yet to the chemical age technology that would introduce gun-powder, they were able to resist somewhat effectively at first. The Taman, not pausing to think and understand, reacted with vigor. When Taman emissaries were killed, the race developed weapons to retaliate in kind. The Kerrblade and the plasma pistol were first. As the remnants of some long-ago military tech, pistols were something that the hive-minds could find a use for. The kerrblade, adapted from a standard surgical scalpel (hence its shape, use, and size), was meant to let the Taman go toe to toe with the orkinoid warriors in melee. The addition of carbon nano-tube armor completed the set. Eventually, the problem with the orkinoid inclusion with the XVI micro-organism was discovered to be the sugar-amino combination, and it was corrected. More orkinoids were harvested to provide initial cultures, and then the entire population was systematically forced to join the hive-mind. To this day, the orkinoids are not trusted by the hive minds--not even the hive-mind present on the Orkinoid's own home-world. This is why it is the Taman who are charged with acting as technicians, and Orkinoids are simple mindless grunts, despite both being equally intelligent overall.
The Shevaar, who were encountered next, provided a slightly different problem. Although the hive-minds learned from earlier examples, the Shevaar were equivalent to 17th century technology, and were fully capable of communcating...and resisting. This was not helped by the fact that the Taman took the "safe" approach, and made sure to launch their campaign in military terms. The Shevaar were, of course, doomed--but their valiant and unexpectedly effective resistance, and their ability to learn to use some of the Taman tech (after watching their brethren use it) earned them the middle-ground between Orkinoid and Taman--they are known to be smart enough to replicate the functions filled by the Taman, but they are still not entirely trusted to be as good as a Taman technician. From this conflict, incidentally, the Taman learned the usefulness of plasma rifles, and grenades.
Now, there are two things to keep in mind, thus far: first, that the Taman had never yet encountered any sign of a fellow hive-mind, and thus they had no idea that such a hive-mind need not be biological; second, that all of these wars were fought at sub-light speeds, using truly enormous colony ships as the Tamans' base of operations.
About fifty years or so ago, the hive minds developed the FTL drive. It is enormously expensive and difficult to produce, and the physics are something that not even the hive minds really understand. What they do know is that, following a previously unexplained anamoly in quantum physics, they've now got something that allows any ship equipeed with these drives to "jump" across large spaces almost at will. Unfortunately, as I said, they are tremendously hard to produce, so the aliens don't have very many yet. For this reason the drives are restricted to carrier ships (much like the one that you shoot down to get your first FTL drive). Most of those are dedicated to exploration purposes, but about two hundred or so are being used for inter-stellar trade and transport.
When the aliens found Earth with one of these ships, they knew what to do--one raid, to get the initial samples of tissue needed to cultivate the XVI virus. After that, it's just a matter of dropping enough Harvester ships onto the planet's surface to infect enough of the natives to let them take over. Because humans seemed a bit more advanced than either race, and because the hive-minds wanted to play with their new toy, about fifty of their new FTL carriers were set aside to carry out the invasion and conquest of Earth. Since initial reports indicated that humans had the final sugar-protein combination to take advantage of all planets the aliens found, their conquest and development was fairly high priority.
The site of that first raid: a city the local humans called Mumbai.
