We now know that the aqir, when broken by their war with the troll empires, split into two main groups, one descending south until it reached the resting place of C'thun and one going north to the region today known as Northrend. Before the great Sundering that split Kalimdor in half, these aqir refugees were already undergoing the process that would render their race distinctive from the aqir/qiraji that they had been and were related to. For some reason, their race altered, and while the qiraji tended more towards semi-humanoid shapes and the silithid ancestors were more waspish or insectoid, the proto-nerubians would begin changing in a way that led them to be more arachnid in appearance, although their massive crypt lord rulership is more akin to scarabs. Since we now know that the ancestral nerubians waged war on and ultimately defeated and enslaved the tol'vir of Northrend, using them as living shock troops, it's possible that the use of the scarab form (seen clearly in Uldum and Ahn'Qiraj, two sites connected to the tol'vir) was a debased form of cultural transference and could have even been deliberate on the part of the nerubians to better control their tol'vir living weapons.
However it happened, we know little about the nerubians between their conquest of the tol'vir and entrenchment in what would be known as Azjol-Nerub and the War of the Spider. We know they weathered the Sundering relatively untouched. We know that while C'thun harnessed their former kinfolk in AQ, they avoided contact with the faceless ones and the Old Gods as much as possible. Their culture divided into its current caste system, with ancient queens giving birth to the scarab/spider hybrid spiderlords, ruling over common workers, warriors and even the semi-humanoid vizier caste, which bears some similarities to qiraji prophets and seems to fill a similar societal role (minus the mad proselytizing for the Old Gods). While they weren't servants of the ancient evils like Yogg-Saron, they were still descended from the ancient aqir, still the ones who came north and enslaved the tol'vir and stole their cities for their own use. Still xenophobic and cruel, still carrying the ancient hate for other races that led them to war with the trolls so long before. It would be that hate that would ultimately doom them.
This eternal cycle came to and end with the arrival of the Lich King to Icecrown Glacier. Although, to be fair to them, the nerubians not only fought against the transformed Ner'zhul and his demon jailors, they actually managed to balk them for a solid decade, keeping them occupied and buying time for the other races of Azeroth to rebuild after the chaos of the Second War and the events that took place beyond the Dark Portal itself. Had the nerubians managed to somehow suppress their loathing for others and ask any of the other races of Northrend for help, perhaps they could well have succeeded in their war with the Lich King. Then again, who would they have asked that would have listened to them? The Drakkari trolls? The wolvar? The oracles? The tuskarr, the tauren, the vrykul? Even without such aid, their natural immunity to the plague of undeath and the leadership of proud and powerful spiderlords like Anub'rekhan and his king, Anub'arak held the Scourge itself at bay.
Even with the cunning of the Dreadlords and the onslaught of crushing numbers of undead, the Lich King might not have taken Azjol-Nerub's Inner Kingdom if not for the mistake of the desperate nerubians, who in their attempt to burrow deeper and outlast their undead foes went so far that they exposed themselves to the ancient and terrible forgotten ones. Trapped between these servants of the Old Gods and their undead enemies, the nerubians died in great numbers. Worse, it was found that while the nerubians were immune to the plague, they were not so resistant to the Lich King's directed necromancy, and soon the greatest of their kind found themselves slaves to a new master.
The Road to Damnation
: The nerubian race, yes. Then the master came. As his influence spread, we made war upon him, foolishly believing we stood a chance. Many of us were slain and raised into undeath. In life I was a king. Today I am a crypt lord.
: In return for immortality, you agreed to serve him. Remarkable.
: 'Agreed' implies choice.
Today, the once-proud nerubians are reduced to undead mockeries serving the Lich King in death, and even when they believe themselves to be free (as Anub'arak did in Azjol-Nerub) they can be raised and forced to serve and fight again and again, trapped forever in servitude. Meanwhile, a small handful of their kind seek to destroy their own former kin who are now crypt lords and crypt fiends and retake their culture from the Scourge.
As to who the surviving nerubians serve, that's an open question.
Wrath of the Lich King bestiary - Nerubian Vizier
The half-spider, half-humanoid viziers once served as advisors, sorcerers, and seers to the mighty nerubian spiderlords. But in the aftermath of the War of the Spider, the tables turned, and in the vacuum of their collapsed society, the cunning viziers rose to power. Utilizing their sorcery and high intelligence, the viziers have emerged as the rulers of the nerubians' underground kingdom.
It is rumored that the viziers themselves may serve an unseen emperor, one who is destined to lead the ancient spider-people to a final victory over the Scourge. While many can only speculate as to the existence of this nerubian emperor, some continue to investigate the link believed to exist between the nerubians and the vicious insect race known as the qiraji.
If they do serve an unseen emperor, we as yet have no idea who he, she (perhaps some ancient nerubian queen?) or it might be. For now, following the events atop the spire of Icecrown Citadel, it has yet to be seen what will befall the nerubians and their quest to free their home.
Next time: the Old Gods themselves.