I’m confused by the timeline of Maegor’s reign. Visenya dies in 44 and Alysanne escapes with J and A to Storm’s End. Maegor kills Viserys as payback, but what was happening in the 4 years between that and Jaehaerys’ coalition deposing him in 48? Maegor had his hands full with the Faith Militant, but wouldn’t a Lord Paramount harboring fugitives from the crown merit a response? Were they all under siege in Storm’s End for 4 years? How was J able to build a coalition against Maegor in that time?

If you get murdered on the Iron Throne by parties unknown, I don’t know if you can call that being deposed…

So here’s what happens between AC 44 and AC 48:

45 AC:

• Maegor’s first wife Ceryse dies, possibly due to illness (a sudden case of maegorius uxoricidelus?).
• The Red Keep is finished and Maegor has the construction workers killed.
• Maegor orders the construction of the Dragonpit. 
• Maegor begins a new campaign against the Faith Militant, is in the field for most of the year.

46 AC:

• Maegor returns from campaign with two thousand skulls.

47 AC:

• Maegor has Ser Theo Bolling executed.
• Maegor marries Elinor Costayne, Rhaena Targaryen, and Jeyne Westerling in a single ceremony.
• Jeyne Westerling goes into premature childbirth, dies not long after. 
• Elinor Costayne survives her stillbirth. 
• Princess Aerea is named Maegor’s heir apparent until he has a child of the body and Jaehaerys is disinherited. 

48 AC:

• Tyanna of the Tower confesses to having poisoned Maegor’s brides, is killed by Maegor’s own hand. 
• Septon Moon and Ser Joffrey Doggett rise up against Maegor, are joined by House Tully, then by the Master of Ships Daemon Velaryon.
• Maegor is murdered on the Iron Throne.