Ever played Spider-Man: Web of Shadows? If you haven't, I recommend it. It's a lot of fun, but it does have its flaws, most notably in the story. Let me explain:

(Note: I'm talking about the story for most consoles, not Amazing Allies Edition)

Anyway, during a fight with Venom, a piece of the symbiote attaches itself to Spider-Man, giving him access to the black costume once more. During the fight, Mary Jane is injured, and an ambulance takes her to a hospital (where Mary Jane gives Spider-Man a present, and calls him "Peter" and no one seems to notice). Anyway, once that happens, there's a random gang shoot out in front of the hospital. This leads to the introduction of Luke Cage, who Spidey teams up with to stop the gang war. Eventually, the leaders of the rival gangs meet to discuss a peace agreement, where Spidey finds about 40 something assassins (and no, I am not exagerrating) who plan to kill the leaders of the gangs to help continue the gang war. Apparently it was staged, but the reason why is never explained. Anyway, after defeating the assassins, we get to an interesting feature in the game: the choices. Choosing the red suit here makes Spidey show the two gang leaders that the war was a set up, and they make peace. Choosing the black suit here makes the two gangs start fighting again, and Spidey has to beta them up, where they're taken to jail. Anyway, after doing either of those, Spidey goes to see the Kingpin. At Fisk Tower (Kingpin's HQ), he finds the Black Cat. After chasing and fighting Black Cat (and meeting up with Moon Knight), Spidey goes to Felicia Hardy's (Black Cat's) apartment, where she confesses her love to the web-slinger. Choosing red suit means you reject Black Cat and meet with Moon Knight; black suit means you stay with Felicia. Anyway, you get missions and such from Black Cat or Moon Knight, depending on your choices, where you eventually fight Vulture. I should note another feature of the game: allies. During the game, you get allies, both heroes and villains. You can use the allies to help you during battles. Anyway, Vulture becomes an ally, and either Black Cat or Moon Knight direct Spidey towards the courthouse, where he stops an attack on it. Then he goes to a rooftop, where civilians (who are infected with symbiotes) attack him. Naturally, Spidey throws them off a building, causing him to be branded a criminal. Anyway, Wolverine tracks down Spidey, and the two fight in Hell's Kitchen. After settling their differences, they decide to fight the symbiotes. Of course, SHIELD comes in and sets up quarantine camps, which Electro goes to, looking for his sister. After a prolonged chase, Electro's sister infects him with the symbiote, and then Electo leaves. Anyway, Spidey goes to a bridge, where the Kingpin asks the obvious question of where the hell are the genius heroes? As it turns out, the plot demands them to be elsewhere. So, Spidey goes to Riker's Island (with the help of either Moon Knight or Vulture, depending on your choices), and, with Rhino's help, breaks out the Tinkerer. Black Widow, the Vulture, Moon Knight, and the Kingpin end up on Riker's, where Spidey tells them to use the Tinkerer to stop the invasion. Anyway, Spidey gets back to Manhattan, where SHIELD blew up the bridges. SHIELD set up a safe zone on the island, and Spidey assissts SHIELD in stopping the invasion, including stopping a symbiote infected Electro, and helping evacuate a church filled with civilians with Wolverine's help...which leads to one of the most awesome things ever to have been concieved: SYMBIOTE WOLVERINE. Anyway, Spidey defeats him, and goes looking for Mary Jane, and ends up finding her and a symbiote Black Cat. After defeating her, and leaving her in near-critical condition, Spidey, depending on red choice or black choice, takes Black Cat and goes with Mary Jane, or does this weird symbiote thing to Black Cat in which she's his slave or something. I'm not too sure. Anyway, it turns out Vulture was infected by the symbiote, and has attacked the device the Tinkerer made to stop the symbiotes. After defeating Vulture, depending on which actions Spidey mainly choose throughout the game, either the device worked, and the invasion is stopped (and Spidey is freed from the symbiote), or the device is destroyed, and Spidey keeps the symbiote. Anyway (I say that a lot, don't I?), it turns out that the SHIELD Helicarrier was infected by the symbiotes, so Spidey, with either Vulture's or Moon Knight's help, goes over there and tries to destroy it. There, Spidey finds a multi-headed symbiote creature I've nickname the Venom Hydra. Spidey fights the Hydra, and Eddie Brock emerges from it. Now, there are, according to Wikipedia, 4 outcomes that can come from what happens next:

"In the good ending, realizing the destruction that has been caused by his alter ego, Brock sacrifices himself. In the bad ending, Spider-man becomes dominated by the black suit and pushes Eddie towards a Helicarrier engine, killing him. The symbiote monster weakens, and the Helicarrier explodes, destroying the Venom symbiote.

Red/Hero Ending : A week after the catastrophe, Spider-Man narrates about his victory on the top of a building before swinging away with Mary Jane, to make her forget he was narrating.

Anti-hero Ending: A week after the catastrophe, Spider-man calls Mary Jane to tell her that he's sorry for his bad decisions, but she doesn't answer, so he leaves this message in her voicemail.

Anti-villain Ending: Spider-Man dominates New York's symbiotes with the power of the Black Suit.

Black/Villain Ending: Spider-Man dominates New York's symbiotes with the black suit, and with a symbiote Black Cat at his side. After this, it is revealed that Kingpin, the Tinkerer, and Black Widow have all banded together to stop Spider-Man, by unleashing a symbiote Wolverine, which Spider-Man defeats earlier in the game."

And that's the game.

Now, there are a few problems with this game, especially with the story, and there's a question that nags at me: Why didn't SHIELD just equip a Helicarrier or something with a sonic gun and start blasting Manhattan? Symbiotes are vulnrable to sonics, and I'm pretty sure SHIELD knows this, since they mention this and it's implied that Spidey has had experience with the symbiotes beforehand. In fact, if I remember correctly, Spider-Man has used a sonic gun against symbiotes before. Now, one could argue that doing so might kill the hosts, but that's only if the symbiotes bond to their hosts like Venom or Carnage's did. I'm pretty sure that there wasn't such a bonding here. Also, the way they defeat the symbiotes in the game is partly through sonics.

Also, why did Venom's symbiote decides to spawn armies of symbiotes and symbiote hives? It has done so before, and I'm not sure it can. Granted, some might argue it's a better premise for a symbiote invasion than the last time such a thing was done, in "Planet of the Symbiotes", where, in the words of Linkara, it was the Venom symbiote's "emo scream" that brought the symbiotes to earth.

Anyway, there are some problems in the story, so I have an idea or so on how to make it better.

1) Have SHIELD plan to create a sonic weapon fixed to the Helicarrier to stop the symbiotes. But, have it so that symbiotes attack the Helicarrier, and the thing needs to be destroyed, which would cause Spidey to go to Riker's to get Tinkerer.

2) Define the relationship between Peter Parker and Mary Jane more clearly. Are they married? Dating? It's never explictly stated.

3) Either get rid of the gang war part, or explain why Kingpin would want to engineer a gang war.

4) Different voice actors for Spider-Man and Black Cat. Spider-Man sounded like he was going through puberty (he at one point says to Venom, "Look at me when I talk to you," causing me to laugh because of his voice), and Black Cat sometimes sounds like she should be Black Cougar.

5) Have the symbiote infect some people discreetly, so that no one knows. However, some people will end up showing signs of their actions being controlled by a symbiote, causing mistrust among the heroes.

6) Continue the game even after the defeat of the Venom Hydra. I personally think it would be cool if, after the final battle, you can swing through a saved New York city fighting crimes and helping the city recover, or swing through a symbiote infested New York you now control, giving orders to some symbiotes to infect those who are uninfected or something.

7) Have Wolverine explain why the other X-Men are absent. I honestly wonder why. Or...

8) Briefly mention that some heroes are trying to stop the invasion. Something similar happened in another Spider-Man story, "Spider-Island", where citizens of Manhattan got Spider-Man-like powers, and then turned into giant spiders. A lot of superheroes were present in the story, but they never really got in the way. In other words, the main focus was still on Spidey.

Honestly, if these ideas were applied beforehand, this already fun game would be a hell of a lot more awesome.