Manhattan, 1:15 AM. The Red Skull has not contacted Crossbones and given the order to execute his latest plan. While one unnamed henchman voices his concern that something has gone wrong, Crossbones is confident that the Skull will call when he is ready. He threatens to kill them if they bring this up again.
In Brooklyn, Steve Rogers awakens from a nightmare. He and Bucky were fighting the Germans during World War II. Bucky was shot in the stomach and died before he could receive medical assistance. He knows that this did not happen and is annoyed when his dreams and memories become intermingled. He then receives a call on his SHIELD communicator from Sharon Carter. She tells him that he's needed on the Helicarrier and instructs him to meet her on the roof of his building in two minutes. She will brief him on the way.
When they arrive on the Helicarrier, Captain America meets with Nick Fury, who informs him that he has the body of the deceased Red Skull aboard the ship. Fury explains that they intercepted a call to the police about this and were able to extract the body before anyone was aware. Both are very skeptical that this is the genuine article.
Since the Skull was placed in a body cloned from Rogers, they need a fresh sample to compare the authenticity of the body. When they enter the lab, they find the Skull on an examination table. Fury explains that the Skull was shot through the heart with a high-powered sniper rifle, which explains the large hole in this chest.
After they obtain the sample, Cap wonders aloud what the Skull – if this is actually him - was doing in Manhattan. He wants to see the crime scene. When they arrive, Fury gives Cap all the details that they have about the state of his penthouse when they arrived. Cap begins to believe that it may be the Skull when he finds a disguise the Skull used. He knows it was a disguise because he remembers seeing that exact face yesterday.
One of the technicians examining the penthouse informs Fury that a display case has an unusual device attached to it. He thinks that it’s some type of receiver with several open feeds, one of which was traced to location in Manhattan.
A short time later, Cap and Sharon arrive at this location, which is in the sewer. As they make their way through the tunnels, Cap eventually convinces Sharon to tell him why she came along. She's following Fury’s orders to determine if Cap killed the Skull. SHIELD is aware that he has been exhibiting more aggressive behavior since the Skull escaped prison. While he is shocked at this accusation, Sharon states that she knows he didn't do it.
As they continue their mission, they find one of the Skull's henchmen wearing a black armband with A.I.D. Written on it. Cap easily overpowers him and learns that they're part of Advanced Ideas in Destruction, a splinter group of A.I.M. This occurs moments before another henchman arrives and opens fire. Crossbones hears the firefight but remains hidden when he sees Captain America.
Cap fights his way through the A.I.D. mercenaries toward their bomb. Even though they activate the device, Cap disables their W.M.D. Sharon calls in to Fury to report their mission's success. Fury then informs her that they ran a thermal scan over the display case from the Skull's penthouse and learn that it housed a Cosmic Cube. Whoever killed the Skull has that in their possession.
Crossbones escapes and calls his counterparts and report that the Skull is dead, but his plan will be carried out.