There are many minor villains in the Marvel Universe with technology-based powers. S.H.I.E.L.D. finally began to think: how can those villains pay the huge costs of their technology, with their small petty crimes?. The answer: because Latveria (ruled by Lucia Von Bardas at the time) is financing them to cause mayhem in the U.S. Nick Fury explains all this to the president, but he is ignored: the president is in good diplomatic terms with Von Bardas. As he was sure that allowing the situation to continue would call for a huge disaster, Fury organizes a secret covert team to infiltrate Latveria and stage a coup against Von Bardas. Those heroes were Captain America, Spider-Man, Daredevil, Luke Cage, Wolverine, and S.H.I.E.L.D. agents Black Widow and Daisy Johnson. And when they had done it, Fury erased their memories of the whole thing, except for the two agents.
All that took place a year back. In modern day, all those who were involved in that operation (but didn't remember) were starting to be attacked, and begin finding clues of what happened a year before. It ends with a big fight against a cyborg Lucia Von Bardas, aided by all the petty criminals who use her technology. She is defeated, and the whole coup attempt is finally outed. Nick Fury then announces to the supeheroes that he will now became clandestine.
Secret War contains examples of:
- Actually a Doombot: The Nick Fury who fought alongside the heroes in the last battle. The real Fury had already departed by then.
- Author Appeal: Nick Fury handpicks a squad of superheroes to invade Latveria. They happen to all be characters Brian Bendis is openly fond of, especially Luke Cage, Daredevil, and Spider-Man. Especially obvious when the files in the supplementary materials show Fury opted to pass on Iron Man for the mission because he'd ask too many questions, which the entire team sans Black Widow and Daisy would do as well.
- Blah, Blah, Blah: Nick Fury found a S.H.I.E.L.D. report to be basically like that. Then he heard that Luke Cage was attacked, and he suddenly become interested.
- Chekhovs Gunwoman: Daisy Johnson.
- Cut Lex Luthor a Check: Finally acknowledged in-story.
- Does This Remind You of Anything?: There is a conspiracy theory that says the Bush administration knew that something like 9/11 may happen, and did not do anything about it. This storyline sets a parallelism, and Nick Fury even mentions that he won't let it happen "again".
- In the introduction for the collected edition, a supposed real life member of the intelligence community mentions stuff like this (intel suggests someone is engaging in terrorism, leadership opts to use it as leverage instead of actively stopping it) happens all the time.
- Harmless Villain: The Killer Shrike had a number of pages with S.H.I.E.L.D. agents mocking on how much of a Harmless Villain he was.
- Hidden in Plain Sight: Invoked when Peter asks Nick Fury if the entire team getting on the same plane was a bit too obvious for a supposedly secret mission. Fury counters that the team travelling under their secret identities are 'just' a teacher (Peter Parker), a lawyer (Matt Murdock), a kid on spring break (Daisy Johnson), a bodyguard (Luke Cage), whatever Logan is and Captain America, on a plane with over a hundred other random passengers; the only person looking that closely at the situation would be Fury himself.
- Invisible President: Nick Fury details a terrorist threat to the U.S., and the president simply dismisses it? They had to use the trope, or face very serious legal trouble.
- Jack Bauer Interrogation Technique: The Killer Shrike had to suffer one at the hands of S.H.I.E.L.D. agents.
- Motive Decay: A rare heroic example: Fury simultaneously decides that this mission to take out Von Bardas must be one that no one can know about so as to protect himself and his team from reprisals AND to use superheroes to make it as big and flashy as possible so nobody ever tries to do what Von Bardas has done ever again.
- On a meta-level, this is lampshaded by the creators who point out that the heroes were originally going to be in normal black ops gear to hide that it was American superheroes invading foreign soil but that would make it harder to figure out who was who for the reader so everybody got variant black ops versions of their typical costumes.
- Nice Job Breaking It, Hero!: Material reveals that the President's plan was to blackmail Von Bardas into cooperating with them, using the evidence of her dirty dealing against her, which was why no action was taken. So, not only did Fury get Luke Cage (and his pregnant girlfriend) caught in an explosion, messed with the minds of people who previously trusted him, but he created a lot more problems for everyone involved, ended up having to go underground, and his successor was set up to fail. Oh, and him not being in charge of S.H.I.E.L.D. provided the Skrulls with an advantage in the lead-up to Secret Invasion.
- Offscreen Moment of Awesome: The big fight in Latveria. We just got a free sample.
- Oh, No... Not Again!: Wolverine does not like people messing with his memory... again.
- Secret War: Obviously. Even more than the original Secret Wars (unrelated to this story).
- Sequel Hook: Of a sorts. The US President's interview with Maria Hill after she's named director of S.H.I.E.L.D. show's him saying that he's never liked superheroes and was looking for a way to keep them in check. This foreshadows the Superhuman Registration Act that would be the centerpiece of Civil War.
- Spiritual Successor: The New Avengers, also by Bendis, an Avengers line-up with more or less the same characters.
- Those Two Guys: Jasper Sitwell and Jimmy Woo become this in the supplementary materials as interrogators to the various villains held. Fury even lampshades this in their files.
- Title Drop: When Steve, Matt, Peter and Fury are discussing the attacks on the team, one of which resulted in Luke Cage being hospitalized.Steve: Tonight's the anniversary.Matt: Of what?Steve: Of our Secret War.
- Victory-Guided Amnesia: But not for this story, for the background story at Latveria.