Hygot refers to the custom Minecraft: Java Edition server architecture used by the Hypixel server network1). Hygot is a fork of Spigot 2), which was itself a fork of CraftBukkit3). Hypixel maintains architecture for modern Minecraft, though this appears to be used exclusively for Skyblock. Most other games appear to run on their older 1.7.10 spigot-like backend, modified by a large number of custom and Paper patches.

1)
On 4 September 2014, Hygot was released because, according to Plancke, “[they] wanted to declutter, streamline, and, above all, optimize it for [their] use case.”
2)
On 4 September 2014, Spigot was taken down due to the DMCA of CraftBukkit
3)
On 4 September 2014, CraftBukkit was taken down due to a DMCA filed on 3 September 2014 by former CraftBukkit contributor Wesley Wolfe