First Appearance: X-Men (1st series) #112
Ever a man of contingencies, Magneto had several facilities scattered across the globe, hidden from the eyes of humans. One such facility was a sprawling complex that he constructed in Antarctica. To the casual observer, this one facility seemed to be many different ones, but all were actually interconnected by tunnels that snaked beneath the icy continent.
The origins of Magneto’s decision to build this secret complex seems to have occurred after Magneto discovered the existence of the Savage Land, a primordial “lost land” in a secluded area of Antarctica, where dinosaurs still lived, 
along with various primitive human tribes. Having just been defeated by not only the X-Men, but also the mighty Avengers, who had teamed up with Magneto’s perennial foes to stop the would-be despot, Magneto had seemingly drowned in the Atlantic Ocean. To his own surprise, he found a maze of caverns beneath the bottom of the sea, which eventually led to the Savage Land. [Avengers (1st series) #53, X-Men (1st series) 63]
With some of the natives possessing genetic potential for mutant powers, Magneto recruited new followers to his cause, and he would return to the Savage Land every now and then to further explore the area and its resources. The creation of his huge Antarctic complex must have happened at one of these later visits, as during his initial stay [from X-Men (1st series) #62 to X-Men Hidden Years #12] Magneto had neither the time nor the power for such a project.
The main section of the base seemed to have been constructed in the bowels of an active volcano just a few miles from the edge of the Savage Land. Over one mile below the surface of the icecap that surrounded the volcano, the complex covered an area of five square miles. Drawing its power from the Earth’s core itself, the underground base of operations was self-sufficient. Also, as it was only accessible through the mouth of the volcano itself, traveling through a retractable dome (through which the above lava was prevented entry by Magneto’s own power), the fortress was impregnable.
How long this facility lay in Magneto’s care is unknown, however he decided to use it as a place of imprisonment for the X-Men. Having captured them at a point of weakness, Magneto constructed a prison of technology, rather than iron bars, within the facility. He placed each of the captive X-Men in chairs, which tapped into their nervous systems, rendering their powers useless. Though it kept their minds as clear as ever, the chairs reduced the X-Men’s physical abilities to those of six-month old infants. For their basic needs, Magneto left behind a robotic “nanny,” which would feed and bathe them. Since the X-Men 
would be unable to escape the heart of the volcano, Magneto left them alone with the nanny. However, later alerted to a malfunction at the Antarctic complex, Magneto returned to investigate and discovered that the X-Men had freed themselves. Working as a team, the X-Men fought Magneto to a standstill, though in the process they also damaged some of the equipment holding back the lava from above. In minutes, the entire complex was destroyed by the very heat of the molten rock that had powered it. Magneto managed to escape via his own powers, returning to his main headquarters, Asteroid M. Beast and Phoenix also managed to make it to the surface with the use of the redhead’s growing cosmic powers, though they believed the rest of the X-Men did not. Months later, they would learn that Cyclops and the others had managed to dig an underground tunnel from Magneto’s volcano complex to the Savage Land, a short distance away. [X-Men (1st series) #112-113]
Years later, yet another section of Magneto’s Antarctic complex would be used by him as a place of recuperation - as well as plotting of schemes. One such period of recuperation 
apparently occurred shortly after Magneto’s purported death at the destruction of Asteroid M. Though he remained hidden for months, Magneto’s convalescence in the Antarctic was still hinted at. For example, when the X-Men’s Blackbird was shot out of the sky and crash-landed in Antarctica, Magneto secretly aided his old friend, Xavier, by providing him with food and shelter in his hidden refuge - without letting himself be seen. [X-Men (2nd series) #3, X-Men Unlimited (1st series) #1, Wolverine (2nd series) 69-71]
When Magneto did reappear, he did so with a vengeance, gaining the space station which he renamed Avalon and used it to threaten the Earth once more. However, after a battle with Xavier, Magneto had been left in a mental vegetative state and was cared for by his loyal Acolytes. Months later, though, Magneto’s orbital facility of Avalon was destroyed by the dimensional refugee 
from the Age of Apocalypse, Holocaust. Still mentally stricken from Xavier’s attack, Magneto himself was taken by the then-Acolyte Colossus into an escape pod.
The pod seems to have been pre-programmed, as it landed within walking distance of a tower that arose out of the Filchner Ice Shelf over Antarctica’s Weddell Sea. However, upon waking up from the crash, Colossus discovered Magneto was nowhere to be found. Instead, he in turn was found by Callisto, who used equipment from the tower’s medical bay to tend to Colossus’ needs before returning him to the X-Men. [X-Men (2nd series) #43-44]
Much later, Colossus and the X-Men would learn that the first recruit into Magneto’s first Brotherhood of Evil Mutants, a cosmic teleporter called Astra, had found and abducted Magneto. She had then used her equipment to restore his mind, after which she created a clone to use against her hated former ally. This clone would eventually be known as the X-Men called Joseph. Despite Astra’s plans, Magneto escaped her clutches and eventually even defeated her clone, who was left amnesiac. It was in this state that he was found by the X-Men and taken in. [X-Men (2nd series) #86]
While the X-Men took in Joseph, believing him to be a de-aged Magneto, the true Master of Magnetism returned to the Filchner Ice Shelf, where he set up base in another tower, which none of the X-Men had seen before. This citadel could be submerged into the sea beneath the ice shelf, hidden from view. There, Magneto could safely plot his next big scheme, as he knew that the X-Men wouldn’t come looking for him as long as they believed him amidst their ranks. Living in seclusion, Magneto built himself another robotic servant, Ferris, and also discovered a strange, sentient energy being, that he placed in a containment tube for further study. [Gambit Annual ‘99]
The X-Men, of course, were unaware of all this, though a small group of the team - including Joseph - unknowingly passed close to Magneto’s position upon returning from a mission in space.
Traveling from the Shi’ar Empire via stargate, Gambit, Rogue, Joseph, Beast and guest Trish Tilby arrived in a cavern located apparently underneath or close by the first of the two citadels. The place looked very familiar not only to Joseph but the Beast, who had a full memory of his incarceration there so long ago, as well as his former jailor: the robot “Nanny.” Whether the original nanny had survived or been rebuilt, the technology to remove the X-Men’s powers was now among her systems, and so she easily captured the X-Men for a brief time. However, as a human, Trish Tilby was invisible to Nanny’s sensors and destroyed her. [Uncanny X-Men #347-349]
Afterward, Gambit surrendered to two bounty hunters, Spat and Grovel, who had been hired to find him. They too had been captured by Nanny but, now free, were determined to bring in the Cajun X-Man to atone for his past sins. Following far behind, the X-Men were shocked when the second citadel rose through a glacier in front of them. Dressed up as Erik the Red, an alias previously used by both Cyclops and a Shi’ar agent, Magneto greeted his “guests” and declared his wish to put Gambit on trial for his crime of having gathered the band of murderers known as the Marauders while in the employ of Mister Sinister. Pressed into service as the jury, the X-Men were indeed horrified, though they refused to allow Eric the Red to execute their teammate. As they broke free, Erik used his abilities to demolish the citadel around them as he himself escaped. Magneto’s plan to maintain his cover and at the same time cause dissent in his enemies’ ranks worked quite well; even though the X-Men saved Gambit, they expelled him from their group, leaving him behind and very much alone in the Antarctic wastes. [Uncanny X-Men #350]
The situation was dire for Gambit; abandoned at the cold, powerless base without any sustenance. Desperate for food, he even chewed off the plastic of some wires. Days went by and Gambit thought he was about to die, until he stumbled upon the canister with the green energy being in one of the labs. Unaware of what it actually was, and having no other options left, Gambit released it and it entered his body, merging with him. The energy gave him a boost, enabling him to leave the base and make his way back to civilization - barely.
Later, Gambit eventually earned forgiveness and made his way back to the X-Men. Several weeks down the road, though, the energy turned out to be a female mutant whose body had been destroyed by itself upon the first manifestation of her powers. Once the X-Men realized something was wrong with their teammate, the energy woman made her presence known by knocking out the assembled X-Men and disappearing with Gambit. After they came around, the X-Men decided to begin looking at the last place they had seen Gambit before he had exhibited a connection with this energy-creature, so they returned to the base in Antarctica. There, they discovered video recordings made by Magneto, thus learning that it was he who had been masquerading as Erik the Red. More importantly, though, Magneto’s files on the energy mutant gave them the means to track her and Gambit down. The X-Men quickly departed, once again abandoning the citadel. Shortly thereafter, the X-Men thwarted the woman’s attempts to bond with Gambit permanently, dissipating her in the process. [Gambit Annual ‘99]
Each of the above facilities appeared in separate stories, and at first glance they might seem to be unconnected. However, subtle references to each clearly link them or establish them to be the same.
All in all, there’re five sightings of Antarctic bases operated by Magneto or one of his servants:
a) the volcano complex in X-Men (1st series) #112-113
b) the mysterious tower in X-Men Unlimited (1st series) #1
c) the citadel in X-Men (2nd series) #44
d) Nanny’s cavern in Uncanny X-Men #347-349
e) the second citadel in Uncanny X-Men #350 and Gambit Annual ’99
Nanny’s presence alone in both the volcano complex (a) and the cavern (d) wouldn’t necessarily mean that these two places are connected - after all she could have been brought to another location in the meantime. However, additionally, the Beast clearly recognizes the remnants of the volcanic complex where he had been imprisoned before. [Uncanny X-Men #348]
An outside shot of the building on top of this cavern (d) shows it to look exactly like the citadel where the escape pod from Asteroid M landed (c). Additionally, in both occasions, the location was detailed as the Filchner Ice Shelf. [Uncanny X-Men #348, page 12, panel 4 / X-Men (2nd series) #44, page 8, panel 1]
The escape pod was programmed to reach a base of Magneto (c), apparently one where he had been to before (b). In both instances did the base have some sort of medical facility where Xavier and Colossus were treated. [Uncanny X-Men #348, X-Men Unlimited (1st series) #1]
Additionally, the volcano complex (a) was only a few miles from the Savage Land, as the X-Men were able to tunnel there by digging, and when the Blackbird was shot down near the mysterious tower (b), it was on the way back from a visit to the Savage Land. [X-Men (1st series) #114, X-Men Unlimited (1st series) #1]
Therefore, the bases listed above under the letters a-d are all different sections of one and the same complex. However, the second citadel, in which the “trial of Gambit” occurred (e), was a snow-cat drive away, clearly showing it to be a different building. Still they might have an underground connection. After all, the architecture is evidently the same [Uncanny X-Men #348, 350] and with the volcano complex covering five square miles, the two citadels might be located on the far ends of it, explaining the surface distance between them.