The story begins at an old Barber Shop at Lower East Side New York City where Wolverine meets Bucky Barnes A.K.A. Winter Soldier. Wolverine tells Bucky that he doesn't believe that Captain America is dead. He compares the Captain America's death to the Barber Shop "things arent always as they seem" due to the fact that the Barber Shop is really a secret SHIELD facility. As Wolverine says this, Bucky clicks a button on the chair he is sitting on and which falls on to another floor. Wolverine follows Bucky down and tell him how not just Captain America but Bucky as well,was thought to be dead before back in World War 2. Bucky then asks Wolverine what he wants in which Logan says he needs Bucks help in getting to Captain America's body and identify it but Wolverine is turned down. Later at hells kitchen Wolverine approaches Daredevil to help with the job that Bucky had turned down earlier in which he agrees. The two are able to get on board the SHIELD Helicarrier undetected and unseen with help from Doctor Strange who gives them a ten minute window. Before going to where Captain America's body is being held Wolverine instead goes to Crossbones holding cell. Wolverine then puts a gun next to Crossbones and begins to interrogate him. After finding out that Crossbones did not get the kill shot,wolverine then taunts Crossbones and a in a fit of rage grabs the gun next to him and shoots Wolverine who strikes back almost killing Crossbones but is stopped by Daredevil. Wolverine then tells Daredevil to leave and makes his way alone to Captain America's body. Reaching there,he meets Iron Man and Hank Pym who both aren't effected by Dr. Strange spell. Wolverine confirms that Captain America's body is real and leaves knowing that Tony needs him to confirm Captain America's death to all those people who are in denial. As Wolverine leaves, he tells Tony that if he had anything to do with Captain America's murder, he would kill him.
The Mighty Avengers are on their way to stop Tiger Shark who possesses Gabriel's Horn which gives the user the power to control sea monsters. Tiger Shark has also used the horn to attack a top secret nuclear warhead installation. Meanwhile, Ben Grimm A.K.A. The Thing of the Fantastic Four arrives at the Sanctum Sanctorum home of Dr. Strange. The Thing is there to play poker with the New Avengers in attempt avert their minds from the Death of Captain America. As the Mighty Avengers arrive, Ms. Marvel orders them to fight of the sea monsters while she deals with Tiger Shark. Tiger Shark tells Ms.Marvel that he had attacked the facility in hopes of defeating the Avengers and not be a second stringer villain. At that moment the Black Widow is about to be crushed but is saved at the last moment by The Sentry. Back at the Sanctum, Wolverine arrives and conforms to everyone Captain America's death making Spider-Man angry and quickly attacks Wolverine. Spider-Man begins to continuously punch Wolverine causing Wolverine to unsheathe his claws but the fight is stopped by Ben Grimm telling them that fighting won't bring Captain America back. Spider-Man then leaves the Sanctum and Wolverine secretyly follows wanting to make sure Spidey arrives home safe. Elsewhere, Ms. Marvel savagely beats up Tiger Shark but is stopped by Namor who points out that she is beating Tiger Shark up to make her self feel better about Captain America's death. Namor then brings Tiger Shark back to Atlantis warning them that they will pay if the secret nuclear missiles were aimed at Atlantis.
Clint Barton A.K.A. Hawkeye is at the Avengers abandoned mansion at New York City. Clint shoots an arrow into the sky to signal for Iron Man who arrives quickly after. Iron Man who is shocked to see Clint scans him to make sure hes real. Clint tells Tony that he has called up Iron Man to talk about Captain America's death, Iron Man replies with a quick punch knocking Clint out. Back at the Helicarrier, SHIELD agents upon finishing tests inform Iron Man that that is the real Clint Barton. After waking up from being unconscious, Iron Man takes clint to a room which holds Captain America's Shield. Clint takes the shield for a test run and proves to be really good at it saying its all about accuracy. Iron Man then tells Clint that the world needs Captain America and offers him the role. Clint is at first reluctant but is convinced when Tony reminds Clint of the changes in costume hes made and that perhaps it has led to this. Elsewhere a Ninth Avenue Roxxon Gas Station is being robbed by Firebrand but is confronted by Young Avenger members Patriot and the new Hawkeye (Kate Bishop). Kate takes Firebrand down with a trick arrow that extinguished his fire while from a far Iron Man and Clint Barton watch and soon after Iron Man confronts Hawkeye and Patriot for violating the registration act much to Clint's dislike. Hawkeye not bothering to explain herself shoots Iron Man with a EMP arrow that shuts down the suit (for more, see Iron Man Armor). The two young Avengers then attempt to escape but are stopped by Clint Barton dressed as Captain America. Patriot and Kate who are offended by the impostor and demand an explanation but Clint defends him self saying that Kate had named her self Hawkeye. Kate, not knowing that the impostor is Clint, says that she took the name to honor the hero and if he was alive would call her self something else. Hearing this Clint feels remorse having used his old friends name and allows the Young Avengers to escape as Iron Man arrives. Clint then tells Tony that he will no longer be Captain America and tells Tony that he deals with his grief by bargaining, hoping that with Clint as Captain America t pain would be less. As Clint walks away, Tony warns him that he will arrest him if he joins the New Avengers. Tony is then left alone in the rain, holding Captain America's Shield.
Following Peter Parker leaving the Sanctum after fighting with Wolverine, stands infront of his Uncle Ben's grave. Over the grave Peter recalls all the previous people he has lost in his life Gwen Stacy, Uncle Ben, Harry Osborn and now Captain America and Peter's blame him self over the role he played in Captain America's death during the Civil War. At that moment his Spider-Sense tingles and Peter finds the Rhino. Without thinking Peter quickly attacks the Rhino who then defends him self. During the fight Rhino breaks his own mothers grave stone and in rage continues to attack Peter who is stunned to find out that he had made a rash and wrong judgment. As the fight continues, Peter recalls one of his fights with the Hulk, as the Hulk was about to crush Peter,he is saved by Captain America and the two are able to defeat the Hulk. Upon realizing that Captain America would not come to save him this time, Peter defeats the Rhino and is joined by Wolverine who had been stalking him since their fight wanting to make sure Peter gets home safe. Peter who wants to be left alone leaves Wolverine and goes to the bridge where Gwen Stacy had died. Wolverine joins him shortly after and tries to comfort Peter, but Peter says that Wolverine has no idea what he is going through. Wolverine then describes in words how Peter feels and then explains to Peter its called "depression" because its "depressing" but life gets better. With that Peter says "Someday" and swings away into the rain.
Thousands of mourners and fans have gather at the Nations Capital to attend the funeral of Captain America who's body is being buried in Arlington National Cemetery where Ben Grimm, Black Panther, Iron Man, Rick Jones, Ms. Marvel, The Falcon bring carry Captain America's casket. His body is put to rest over a large statue of Captain America sculptured by Alicia Masters. Later, Tony speaks for Captain America but upon standing there can not bring him self to say the words and leaves saying "it wasn't suppose to be like this" in which Ben Grimm roles his eyes. The next speaker is Sam Wilson who tells everybody the honor he had in being Captain America's partner. Sam then asks everybody who was saved by Captain America in World War 2 and the heroes Captain America teamed with in World War 2. Sam then tells them how amazing it is that everybody here is of a different raise but have all been united by Captain America at this day. Elsewhere, the New Avengers watch the funeral on TV and are saddened by the idea that they could not attend their friends funeral. Three days later in the Artic, Iron Man, Hank Pym and Wasp bring the real Captain America's body and reveals that the one in Arlington is fake for the public. As Tony tells Captain America the things he could not say in Arlington he is interrupted by Namor. Namor arrival was arranged to bring Captain America's body back to the seas where he was first found. Namor then swears that no one shall disturb Captain America's peace while he still rules the seas. Captain America's casket can then be seen sinking deep into the ocean.