The aftermath of the Skrull Invasion has exacted a heavy toll on Captain America, in multiple senses of the term. The Avengers respond to a call from Ellis Island that the memorial statue of Cap and Bucky has been defaced by an angry mob. The negative public perception of Cap is further fueled by inflammatory articles in the Daily Bugle with headlines like "Captain America Traitor!" and "Captain America Benedict Arnold!" Tony Stark goes to the Bugle's publisher J. Jonah Jameson to demand that he stop printing the smears but Jameson flatly refuses until Stark finally relents and gives him an exclusive interview with Captain America himself. He puts Betty Brant and a certain freelance photographer named Peter Parker on the job.
The Cap is escorting Madame Viper and Cobra to the Baxter Building for transfer to 42 and has to feel the full abuse of an angry mob so understandably, he's not exactly forthcoming when Betty tries to interview him about the circumstances. Suddenly the convoy is attacked by the rest of the Serpent Society in a bid to free their comrades. Cap, Hawkeye and the rest of the S.H.I.E.L.D. agents return fire and Peter is able to slip away in the confusion, then swing back onto the scene as his alter ego, the Amazing Spider-Man! His heroic entry is cut short by a cave-in that sends the convoy and everything nearby down into the abandoned flood control tunnels beneath the New York subway.
Trapped in the underground with wounded S.H.I.E.L.D. agents, the prisoners, and a group of hostile civilians, it is up to Cap and Spidey to lead them all to safety while the Serpent Society could be back at any moment.
- Ascended Fanboy: Spider-Man is a huge fan of Captain America. Turns out that Cap has been reading up on Spidey and thinks highly of him, too.
- Clear My Name: Not only following the events of "Secret Invasion", but forming a convenient Plot Parallel with the predominant theme of the Spider-Man mythos.
- Doting Parent: Implied with Jonah. When listing occupations of those he considers real heroes, the first is astronaut (the profession of his son, John).
- Hero with Bad Publicity: Cap in spades. Tony points out that Jonah's been doing the same to Spider-Man for years, which happens again in the end.
- Jerkass Has a Point: Obnoxious as he is, Jonah is right that the Avengers and other costumed heroes are vigilantes who aren't above the law.
- My Significance Sense Is Tingling: Guess who.
- Mythology Gag: Cap's triangular shield is based on the one he originally used in the comics before getting his more famous disc-shaped one.
- The speech that Captain America gives to Spider-Man is very similar to the speech that he gave to Spider-Man in Civil War.
- Not So Above It All: Spider-Man intends to web Jonah's mouth shut for his latest smear.Cap: I'm okay with that.
- Spanner in the Works: The Serpent Society's goal is to free their captured comrades, but just as Anaconda is about to get to Madame Viper, she gets distracted by the others fighting Cap and Spider-Man.
- Special Guest: Spider-Man!
- Spider-Sense: Spidey detects incoming trouble from the Serpent Society, saying it's all around them.
- Ungrateful Bastard: Cap gets a lot of grief in this episode.Madame Viper: Look how easily the people turn on their heroes.
- Whole Plot Reference: To the '90s Sylvester Stallone movie Daylight.
- Wide-Eyed Idealist: Cap doesn't fight back against the accusations, saying he's certain the truth will come out eventually.