Pay close attention to the 2010 Iraq scenes, which clarify why Alex's brother was targeted and how Reese's "code" has evolved.
The code the Machine sends to Finch translates to an Emily Dickinson poem , "Cocoon Above! Cocoon Below!", symbolizing transformation. "Person of Interest" Truth Be Told (TV Episode 2016) - IMDb Person of Interest 5x3
Alex is investigating the death of his brother, Paul Duncan , a soldier who Reese and Kara Stanton interrogated (and Reese eventually killed) during a 2010 CIA operation in Iraq. Pay close attention to the 2010 Iraq scenes,
The Machine sends Root to work as a courier driver. She discovers Samaritan is using the courier service to spread malware via physical equipment. "Person of Interest" Truth Be Told (TV Episode
This episode is a deep dive into Reese's morality and the consequences of his actions as an operative.