Allen was introduced in "S.S.D.D.", helping Sergeant Foley train Afghan National Army troops at Firebase Phoenix in Afghanistan. He demonstrated to the troops how to aim, fire a weapon, throw a grenade to take down targets. He then underwent a selection phase for Task Force 141, running "The Pit", prior to engaging local OpFor troops immediately afterwards.
After completing "The Pit", he is hand-picked by General Shepherd to go undercover in Vladimir Makarov's personal cell under the alias Alexei Borodin. Allen is eventually killed by Makarov when attempting to escape from Zakhaev International Airport in the level "No Russian", having learned about his real identity ahead of time. He became a victim of a conflict of goals between General Shepherd and Makarov.
The name Alexei Borodin might be a reference to the first Call of Duty game, because of the fact that the first playable Russian character's first name is Alexei, and the first person the player meets has the last name "Borodin".
He is one of the four playable characters in the Modern Warfare series to meet Vladimir Makarov face-to-face.
The tattoos on Allen's chest that were added as part of the operation are Russian Prison tattoos. The cathedral is symbolic of how long a person has been in prison, with each steeple representing a sentence.
He is the only playable character in the Modern Warfare series to be in three factions.
Joseph Allen is mentioned in Call of Duty: Modern Warfare 3 during the cutscene before "Turbulence", on a sticky note that reads: "Who is Alexei Bodorin?", the alias being misspelled.
Furthermore, a cut-off picture of him is seen in the intro cutscene of "Dust to Dust".
Along with Paul Jackson, Andrei Harkov, John "Soap" MacTavish, and Yuri, he is one of the five playable characters to be killed by Vladimir Makarov.
During Yuri's No Russian flashback in the mission Blood Brothers, after going up the elevator it is possible to spot a 5th terrorist, it is possible that this is Joseph Allen, whoever it was he reuses the same character model as Lev.