Skyrim:Containment

Quick Walkthrough
# Find the Arch-Mage.
# Defeat the magic anomalies attacking Winterhold.
# Report to Mirabelle Ervine.

Detailed Walkthrough
right|thumb|College members mourning the death of the Arch-Mage
Tragedy at the College
As you regain consciousness after witnessing part of the battle between Ancano and the Arch-Mage Savos Aren, Mirabelle Ervine will be standing above you, telling you to get on your feet. Gather your wits and find her visibly shaken and upset. Tell her you feel ok, and she will tell you that Ancano is doing something with the Eye of Magnus and that the Arch-Mage is missing. This will begin the quest.  Head to the College's central courtyard where you will find the Arch-Mage's body and a group of mages. Tolfdir will approach you and inform you that whatever killed the Arch-Mage has also affected the town of Winterhold. He asks you to go there and save the town.

No Time for Grief
Cross the bridge, where Faralda and Arniel will be waiting. Faralda will inquire about the situation. Explain that Winterhold is in imminent danger and proceed to the town. Faralda and Arniel will follow and assist you in the battle that awaits.  You will find the town has become infested with a swarm of magic anomalies—fast moving balls of energy  whose attacks deliver frost damage. They explode upon defeat, leaving behind soul gems in their "ghostly remains". Faralda and Arniel prove valuable allies in this battle and, with their help, you defeat the ten anomalies and secure the town. Arniel will remain in the town while you return to the College to report back to Mirabelle.

The Staff of Magnus 
When you find Mirabelle, she will tell you that she and Tolfdir are trying to keep the Eye contained, but are in dire need of the Staff of Magnus. When you tell her that you must venture to Labyrinthian for the staff, she softens a bit from her concern and grief. She intimates that Savos Aren had just recently given her a mysterious torc, cryptically telling her that she would know what to do with it when the time came, and she believes it was meant for you. She also gives you Savos Aren's amulet to aid you on your journey, believing that you will be better served by it.  The Staff of Magnus quest begins here.

Notes
If your horse is stabled within the city, the anomalies can quickly surround it and kill it. Simply rush down there at the start of the quest, hop on your horse, ride it out of town, hop off, and then sprint back on foot and join the fray, unless you have Shadowmere, then he can probably stay with you in the fight.
At higher levels, the anomalies can be used to train Restoration very effectively, due to their large numbers and low attack power.
The souls of magic anomalies are leveled.
All College NPCs will either disappear or lose all dialogue options until the next quest is finished, which temporarily prevents you from advancing certain quests or using College services. Any NPCs who have been made followers or stewards  will also lose their dialogue options until the quest is complete.
You cannot loot the Arch-Mage's body.
If you leave a follower somewhere away from the college or the town of Winterhold, when you go to speak with Mirabelle they may be there.
Enthir travels to Winterhold on Tirdas and Turdas at 10pm and stays there until midnight, even while this quest is active. This means that if the battle takes place during this timeframe, he may join in on the fighting and be a useful ally as an essential character.  
Even after finishing the quest and talking to Mirabelle, magic anomalies will appear in the town of Winterhold and attack the guards.
It is advisable to finish sub-quests involving the townsfolk before triggering the anomalies, as they are known to kill NPCs in town.

Bugs
 
Fast traveling back to the town may fix this.
Also, entering another cell such as the inn can cause it to move out of the wall.
 
 
 
 Entering the console command   will start the quest if talking to Savos Aren does not update the previous quest and Mirabelle does not give the quest.
 To get the quest to start, complete all Winterhold related quests that you have active including any under miscellaneous quests.
 
Wait for an NPC to enter and fix the door for you; saving and reloading won't fix this.
It may also be possible to reset the door yourself by clicking around or near the edges of the door.
 

Quest Stages