- Archive Binge: Reading only main comics will leave you utterly lost as to how the hell Norman Osborn become a Villain with Good Publicity. You need to read Deadpool and Thunderbolts to understand that.
- Fridge Brilliance: The whole story becomes a lot more forgivable if you picked up on Bendis' continual dialogue that the Skrulls have absolutely no honor, and that for all their troubles (and a grand plan whose first step relied solely on the abilities of a Spider-Man B-list villain)—they still underestimated Earth's Mightiest Heroes (as it turns out, on a vast scale), and weren't as clever as they thought they were (or else completely outclevered) at the end of all things. Reed Richards even lampshades their lack of creativity at one point: for all their power and effort, they still hid behind shapeshifting and he was still able to figure them out. Basically, it's either a greatly expanded version of Fantastic Four #2—a comic which came out before there was even an Avengers comic book—or an equally expanded version of the Kree-Skrull War (incidentally, a story which Bendis remains highly fond of).
- Fridge Logic: For a long time, Jessica Drew's status quo was that she'd lost her Spider-Woman powers. Then one day she turned up with powers even stronger than before and joined the Avengers. She eventually admits that Hydra had offered to restore her powers in return for spying on the Avengers for them, and she accepted, but only pretended to spy on the Avengers while actually spying on Hydra for S.H.I.E.L.D. and ... it's complicated. Anyway, when it turns out that Spider-Woman is actually the Skrull Queen Veranke, a flashback shows that the Hydra agents who offered to restore her powers were actually Skrulls, and that after they anesthetized her to perform the operation, they swapped in Veranke. Basically, powerless Jessica goes into the operation room, and Veranke duplicating Jessica's old powers comes out. So, once the Skrulls are defeated and the captured heroes are released ... why does Jessica Drew have powers? Did the Skrulls go ahead and perform the operation anyway? Why on earth would they do that?
- The Hydra Skrulls really did restore Jessica's powers. They couldn't have had Veranke replicate them otherwise (It had been shown that the Skrulls' use the blood of their captives to take on their perfect disguises, powers and all).
- Heartwarming Moments: Ms. Marvel's hug to Spider-Woman and assuring her that the heroes that's looking at her with suspicion was just merely confused.
- Hilarious in Hindsight: Discovering that Hank Pym had been replaced by (multiple) Skrulls well before Civil War ever happened makes the part where Hulkling knocks him out and replaces him to free the Anti-Registration heroes both incredibly weird and incredibly funny.
- Idiot Ball: There's approximately an Idiot Ball for every character with dialogue in this story, but the greatest one is Veranke's — she assigns a Skrull to replace Hank Pym, and when he explains why the invasion won't work, she kills him. Then she replaces him, and the same thing happens again, until the third Skrull!Pym is finally smart enough to lie to her. Keep in mind, Hank is one of the smartest characters in the Marvel Universe, up there with Reed Richards and Tony Stark — when a guy like that tells you that your plan isn't going to work, you listen to him.
- Cages Leeroy Jenkins moment in the early part of the story effectively grounds both Avengers teams on the Savage Land while the Skrulls have their run of Earth with little interference.
- One of the biggest crowners goes to the Skrulls' plan to get rid of the Sentry. Their plan is to make him feel that he somehow instigated the Invasion so that his dark half, the Void, would take over and leave them alone. Again, their plan is to intentionally bring out the Void. To the surprise of no one besides the Skrulls themselves, this plan backfires spectacularly.
- Moral Event Horizon: The killing of Wasp is enough to rile every single hero into targeting Veranke's head... then Osborn's the one who gets the kill shot.
- Paranoia Fuel: Anyone can be a Skrull. At least that's how the hype wanted this to look.
- Tear Jerker: Poor Pym, after being freed. This even continues in the subsequent issues of Mighty Avengers.Pym (to Tony): YOU KILLED JANET!! YOU KILLED CAP!! HOW COULD YOU!!?
Bobbi: We really wanted that kid. And October 12th...That...would have been a nice day.
- Clint tests the newly returned Bobbi with October 12th. The next few panels reveal that she was pregnant at one point, but lost the baby. It gets even worse when it turns out that she's a Skrull.
- They Wasted a Perfectly Good Character: Crusader. His story are of moving from Skrull spy to Becoming the Mask and decide that he actually liked Earth was well received and readers were interested in him. His death, which was not only sudden but at the hands of the comparatively boring C-Lister 3D Man was one of the major let-downs of the event.
- They Wasted a Perfectly Good Plot/What Happened to the Mouse?: More like Wasted Perfectly Good Motivation. In What If?: Secret Invasion, we never see any of the characters who already had been or would have been replaced by the Skrulls, nor anyone close to them, and they're never mentioned by either side of the conflict. You'd think that if something good had happened to them, the Skrulls would be using it for PR, and if something bad had happened to them, the resistance would be using it to undermine the Skrulls' public image, but nope. Nothing.
- Much of the build-up was around the concept that the Skrulls this time around would be much less direct and more discrete, sowing instability and chaos into Earth's ranks. While a little of it does happen, the story itself is a fairly standard Easily Thwarted Alien Invasion.
- Crossing over with Plot Hole, Richard Rider sent a warning about the Annihilation Wave to Reed Richards during Annihilation. Earlier in that event, the SuperSkrull appeared on Earth and had an extended conversation about the event with Richards, as well. So the fact that Iron Man, Richards's other major collaborator on the SHRA, was completely in the dark about this universethreatening horde heavily suggested that Richards might have been a Skrull intending to keep Earth from mobilizing against a potential invading army. This would also explain why Richards had shifted his position on superhuman registration since the last time such a bill was introduced and provided a highlyplaced spy among The Illuminati. Instead, it turned out that Hank Pym was the Skrull among the main SHRA supporters and Black Bolt was the Illuminati spy, a move which left Richards's change in postion and bizarre failure to alert the heroes of Earth to the Annihilation Wave (especially since it was headed by one of his personal enemies) completely unexplained. It's even lampshaded in an early issue of Nova's book.
- Unintentionally Unsympathetic. Hawkeye gets some of this for literally murdering the non-threatening Mockingskrull in a fit of rage. She may be an Expendable Clone, and even an alien, and under the circumstances it's somewhat understandable that he is upset, but she's still a person — And moreover, literally a perfect copy of his wife, who wishes him nothing but good. Surely there were other possible solutions, if she was even a problem or threat in the first case.
- The Woobie: If you think Spider-Woman has been a woobie since her earlier runs, watch as the epilogue of this arc dials her woobie-ness Up to Eleven (look on the main page). Also, as much as Pym is often the Butt-Monkey, the epilogue is where his misery just can't be taken for comedy, as just after he's freed from his imprisonment, he had to face the bitter truth of Wasp's death, and everything that took place while he was captive (House of M, Civil War, the death of Captain America, World War Hulk, and the specifics of Secret Invasion itself).
YMMV / Secret Invasion