The comic starts with Iron-Man giving an after-battle pep talk to his Pro Super-human Registration Act (SHRA) SHIELD operatives. He has no qualms calling the fight bloody, as it was, but he reminds everyone it was necessary to sustain the roll of Super-humans in society.
Tony Stark draws his speech to a close, but he tells everyone they will be transporting the captive Super-humans to a more suitable holding zone, and that they would obviously get some interference from the rebels. Tony draws Spider-Man aside, noting he's been very quiet, and asks why. A conflicted Peter Parker brushes off the question, saying talking won't transport the prisoners, and the two get going.
As Spider-Man crouches ready to pounce on top of one of the convoys, he draws in the crowd, half protesting, half supporting. He tunes the frequency of his new suit, picking up both Police and Fire CB radio. Iron Man then remarks that Spider-Man is very useful for his ability to know danger before it has presented itself (via his Spider-Sense). Spider-Man draws in, as he realizes that his new suit that Iron Man made for him must observe him and his powers, as Peter never revealed his Spider-Sense.
Peter Parker's train of thought is interrupted, as he starts to sense a vague danger ahead of them, and underground. Tony takes immediate action, moving the convoy onto a backup route. The secondary route is blocked by protesters, so now the convoy is speeding down a third route. As the convoy is barreling down Yancy street (an adamant anti-SHRA neighborhood), Parker's Spider-Sense acts up, and a white noise seems to appear as minor dangers (people throwing rocks, tomatoes, etc) sets in. But out of the white noise, comes a very pronounced danger -- missiles.
The missiles are destroyed, but the anti-SHRA rebel heroes spring forth, ambushing the convoy. A huge battle ensues, and Spider-Man is picked by Captain America. The fight is intense, Spider-Man steadily losing ground, until he webs down Captain America's shield, only to be immediately bludgeoned. Spider-Man draws back, putting some distance between the two. His webs are ineffective, the Captain easily avoiding them. Spider-Man dives in, letting his new suit's extra pincer arms come out, and they successfully slash at Captain America's face. The two wait, a silence takes over, but it is soon devastated by a distant boom, where the main battle is taking place.
Spider-Man looks back, to see Captain America gone. Dumbfounded, he just stands for a while, before a few teenagers run over, and try to peel away Spider-Man's web to get to Captain America's shield. Spider-Man scares them away, then webs the shield to a wall, a few stories up, saying that nobody should touch that shield, nobody but the Captain.