Though queen Alys' coronation would be mired by controversy and outrage from many of the Stark cadets (in part because many of them chaffed at the thought of being ruled by a woman, something which was still revolutionary even in the more egalitarian north).
However, she would end her reign as one of the more fondly remembered Winter monarchs, in part because of her extensive reforms in both politics and economics and partially because of her exceptionally long reign as queen which lasted almost 80 years, marking her as having the longest reign of any Stark (disregarding those whose reigns are shrouded in myth like the reign of Brandon the Builder.)
At the beginning, however, it didn't seem that way for her first years as queens coincided with one of the harshest and longest winters in the North's history which combined with the catastrophic die-off of cattle throughout the North, later discovered to be caused by a parasitic fungus that sapped the beasts' strength and made them unable to bear the harsh weather.
The famine would test the limits of Northern cohesion and saw many a commoner uprising and lordly rebellion which despite being soundly defeated in most cases still strained supplies and food stores and the few that were successful would ultimately need to be made to stand down through less violent which still tended to be costly in terms of money and resources.
The North was forced to import food from Essos and the Reach at great costs and even that was not enough in many cases; many towns and villages would be abandoned and/or depopulated. Thousands of Northerners would even flee to Essos, particularly to Andalos which had grown by then into a prosperous if fractious realm of rival petty kingdoms through Northern populations exist in all the major Essosi cities from Bravos to Lys and even some making it to the Bazeilik's isles (the tale of how they got there is one often compared to Nymeria flight from the Rhoynar
The queen did as best she could in these circumstances and though she had to make a lot of questionable decisions, the North ultimately survived if only barley and it would never repeat the same mistake again.
One of Alys' first major acts was to sponsor the building of an institute dedicated to improving the North's food security and researching better methods of agriculture and animal husbandry.
It would be those working in this institute who discovered the cause of cowblight and formulate a cure for it, in addition to pioneering four-field crop rotation and extensive greenhouse complexes in the North. Something more radical was the codifying of the basic laws of genetics as a result of observations from experiments aimed at improving certain crops' survivability in cold weather. Though their work would take decades for its full potential to be realized it would establish the nucleus of modern Northern agriculture
More directly, the queen also oversaw with the help of bravosi advisers the implementation of a sub-treasury system though one aimed more at maintaining food stores than controlling prices like the system that will be implemented in the Reach decades after.
More sinisterly was the reconquest of the recovering Riverlands, in no small part for its still quite fertile lands. Though the queen did not directly order the expulsions and forced conversions of the Riverfolk, she knew of and was apathetic to them, so long as it didn't cause problems to consolidation or provoke an attack from any of the Southen kingdoms.
To this day she is hated among Riverlander communities that have taken root in the other six kingdoms as a monster who drove them out of their lands in stark contrast to her almost saintly image among the Northerners. Though the High Septon called for a crusade, none of the rulers of Westeros answered him; at this point, the influence of the faith was beginning to wane throughout the South and thus without any support his faith militant orders were reduced to merely raiding the frontier.
The first half of Alys' reign would be marked by internal reforms and restructuring; in addition to her aforementioned efforts to improve Northern food stores, she established the first kingdom-wide school system and the first true hospitals in every Northern city, most of which are still operational today. Her primary achievement in politics would be the establishment of the Northern Parliament, though ironically enough this was partially forced on her by a rebellion of a coalition of cadet stark houses (the Greystarks being most prominent) who felt that they have been neglected during the famine and as part of their conditions to submit wanted to have some method of bringing their issues directly to the Stark monarch.
The parliament of lords was a haphazard affair at first but it would develop and grow into the well-organized system it is known as today in times and though Alys would initially despise it as a leash around her neck, she ultimately learned to use it to her advantage and served well enough in pacifying the Riverlander population by giving their petty lords the illusion of being involved in governing the Northern Empire (though that illusion would turn to reality in a century).
The Second half of the queen's rule would be marked by her efforts to reopen relationships between the North and its fellow Sunset kingdoms. In addition to strengthening ties with Bravos and the Freehold, he negotiated an alliance between the Westerlands, the North and the Iron Isles in what become known as the "Western Sea Alliance". The alliance was both militaristic and mercantile in nature with the Northerners allowing easy access to Essosi goods for the Westerlands, the Westerlands providing the same when it came to goods from the southern kingdoms and the Ironborn fleets providing security to merchant fleets going in between (to simplify things the alliance was much more complex than merely that but alas this document is too short for that.)
This alliance would be the queen's final major achievement as her health began to deteriorate and though she would rule for another two decades most of the day by day matters were handled by her daughter and heir: The future queen Marila. It was during the final year of Alys' rule that a disaster so great in scope that it would leave no corner of Essos untouched happened.
The Doom of Valyria had come.
A/N: Two chapters remain before this story reaches its end, next part will be the Doom and Aegon's conquest and the final part will be the status of each kingdom by the time ASOIAF begins in canon.