This episode was very emotional. Amaro got thrown to the wolves from the very cop he tried to save.
Now that Cassidy is an internal affairs detective, Lt. Tucker decided to make this his first case -- putting a strain on Brain and Olivia's relationship and pitting Olivia between her life partner and work partner.
As much as I felt sorry for Amaro, at times I just wanted to slap him in the face for running his mouth. It may be over-acting from Danny Pino or the director just wanting his character to be that annoying and hot-headed. Although the plot was great, and if the same thing happened to Fin or Rollins, it wouldn't work. Amaro was a perfect fit; the tough guy that always tries to do everything right ends up being charged with shooting an unarmed 14 year old boy.
Saying goodbye to Captain Cragen, a Law and Order veteran, was hard. In spite of this, the writers were able to make his exit a very graceful and noble one, as well as a powerful passing-of-the-guard moment between Captain Cragen and the newly appointed Sergeant Olivia Benson.