The info we have is from the Infernal City novel, which takes place 40 years after Oblivion, and thus 160 years before Skyrim. Here's what's mentioned in the book:
-with the end of the Septim line, the Empire fell completely apart.
-with the loss of imperial support, the Mages Guild (and I would presume, the Fighters Guild) also fell apart.
-a warlord named Titus Mede managed to capture the Imperial City and crown himself emperor. By the time of the book, Mede had just managed to reunite Cryodiil under his rule.
-Mede replaces the Mages Guild with two new organizations: the College of Whispers and the Synod.
-a good chunk of Morrowind is destroyed when Vivec's enchantments holding the Ministry of Truth frozen in time finally fail, leaving it free to crash into Vivec City, which causes a chain reaction that causes Red Mountain to erupt. The surviving Dunmer flee the province, many fleeing to Solsthiem.
-the Argonians of Black Marsh, seeing Morrowind's weakness, decide to strike back against their historic oppressors, and invade southern Morrowind.
-Elsewyr falls apart into independent city-states, after someone assassinates the Mane.
-Summerset captures Valenwood, forming a new Aldmeri Dominion.
From what we've been told since Skyrim was announced, it sounds like, in the time between the book and Skyrim, the Empire managed to retake Skyrim, which lasted until the High King of Skyrim dies, triggering a civil war in the province.