"The Avengers Protocol, Part 2" is the second episode of the first season of Avengers Assemble, and the second of the overall series. It premiered on Disney XD as part of the one hour, two episode long pilot movie on May 26, 2013.
In a snowstorm, Hulk emerges from a pool of snow before being told to get them topside. He grabs Hawkeye and Black Widow while Falcon flies behind and throws the two onto the snow, with Black Widow landing gracefully while Hawkeye lands on his hands. Hawkeye says good Hulk before telling him that next they would play fetch and go smash. Captain America is referring to Iron Man by his last name while telling him to stay with him. Tony questions how a guy is supposed to pass out in peace with him yelling like that. Captain America asks Falcon how Tony is holding up. The former tells him that if he were a car he "would be a—" before being cut off by Tony, who intervenes by stating that he would be a really cool car.
Falcon realizes that Tony needs medical attention before asking Captain America where the Quinjet is. Hulk tells him that it is buried as Thor moves near it and states that M.O.D.O.K. and the Red Skull met their arrival enthusiastically. Black Widow opts to use her own ride, telling the Avengers to just promise not to rip the leather. While aboard Black Widow's ride and squeezed by the Hulk, Hawkeye questions if he should be outside jumping before Black Widow tells him to deal with it and confirms that there is a hospital nearby. However, Falcon tells her that a hospital will not cover him properly and that Tony's armor was the only thing keeping him alive, specifically the arc-reactor. Tony tells Falcon to get him to the mansion before Falcon questions if he is sure and tells him that he is not sure it would be possible before Captain America welcomes him to the big leagues, stating that impossible is what they do.
While the jet takes off in the snowstorm, Tony begins to lose consciousness again before Falcon reports that his vitals are dropping fast and Captain America starts to call his name out in despair. The Avengers arrive at Avengers Mansion, where Tony is placed in a room and soon has plugs placed in his chest by Falcon. After being shocked, Tony tells them that was something he would never want to do again and sarcastically thanks Sam for not electrocuting him on his first day as an Avenger, whom is told by Captain America that Iron Man has a difficulty with saying thank you. After Tony thanks Sam, he is requested to say it again so the young Avenger can have his voice as his ringtone. Following his rookie remark, he orders JARVIS to deploy the Mark 50 before JARVIS tells him that it is not ready, causing Tony to again order it. After getting standing support from Black Widow and Captain America, Tony thanks Sam and tells him that he can be nice when he almost dies.
Falcon then asks if that means he gets an Avengers membership card, causing Hawkeye to remark that just what they needed was a Stark fanboy with delusions of grander. Meanwhile, Red Skull and M.O.D.O.K. plan their assault on the Avengers, with the latter deploying Microbots on the team and sending them to the Avengers Mansion. After making clear his plans to disband the team due to Captain America having not been killed, Iron Man experiences rejection from his angered teammates and soon is questioned by Captain America if he is serious after having seen their fight against Red Skull. The Avengers separate, with Black Widow going with Hawkeye and Hulk with Thor. However, this downtime is stopped when M.O.D.O.K.'s Microbots come into effect as Hulk starts to senselessly beat on Thor, whom at first was having a nice sparring round in their old training room.
After observing Thor and Hulk fight, Black Widow and Hawkeye gain a hold of the infestation and start to fight each other. Captain America and Falcon arrive to stop them, not realizing they can become affected by merely opening their mouths for a moment. After Captain America becomes infected, Iron Man warns Falcon to get out of there before the latter is also infected and starts to throw down with Captain America, whom asks him if he thinks he is anything except for Stark's prime parakeet while the mind-controlled Falcon insults his age.
Iron Man reverses the effects of the Microbots on all of his teammates. He sends Hulk to "smash" M.O.D.O.K. while the rest of the Avengers take care of Red Skull. The members take turns attacking Red Skull until he takes M.O.D.O.K. and flees. Then, Iron Man discovers that the Mansion's reactor will explode and destroy Manhattan in 90 seconds. Thor and Falcon ushe speed and electricity to create a vortex to send the reactor into space. Black Widow, Hawkeye, and Captain America evacuate civilians. Hulk throws the reactor into the vortex and Iron Man blasts it to propel it farther. Falcon passes out in mid-air and Thor flies to save him while keeping the vortex going. They successfully get rid of the exploding reactor. Afterwards, Red Skull recruits a team of villains in a similar way to Iron Man reuniting the Avengers earlier. His message is intercepted by S.H.I.E.L.D. and Iron Man makes the team aware of the possible threat. Since the Avengers Mansion is destroyed, they move into Iron Man's house. They get a call about a trouble with the Great Wall of China and go to answer it in their new vehicle: the Aven-Jet Prime.