This may spoil the ending somewhat but it makes no sense without it.
Charles Xavier has been transformed into a new being called Onslaught. During a previous battle with Magneto in which Xavier reached in and shut Magneto's mind down, some of his personality "jumped" into Xavier's mind and slowly merged with his repressed anger toward humanity. This resulted in the Onslaught personality, determined to destroy anyone who may stop his plans of world domination. However the Avengers have another set of problems right now.
While Edwin Jarvis cleans the gardens behind Avengers mansion, a man named Tyfon arrives from the future a la "Terminator" (but with clothes on thankfully) to warn him that the Avengers will be killed today by their greatest foe - and only he can prevent it.
This enemy - whose identity was lost over the future years - has opened a portal to a dark dimension where s/he is drawing shadow matter to create the Avenger's other enemies in order to kill them while simultaneously transforming the Earth into a shadow state. Using future technology Tyfon is able to directly interface Jarvis' mind with their computer system to find out who it is.
The attacks on the Avengers become increasingly difficult to handle and they become separated by the swarm of past enemies.
Having the weight of the world on his shoulders, Jarvis' attempts to list their enemies from the beginning is rejected by an increasingly angry Tyfon. Jarvis infers that Tyfon is actually Loki and makes him mad enough to reveal himself through not-so-subtle implications that he isn't a worthy adversary. Loki informs Jarvis that by channeling his memories through his magic "device" he has helped to bring about the defeat of the Avengers and the end of the world. As a last ditch effort to save them, Jarvis issues a full priority summons on his Identicard.
The Avengers abandon their respective battles and return to Avengers mansion and discover Loki standing poised to take over Earth with the energy from the other dimension boosting his own power, transforming the Earth into shadow matter at an increased rate. As a final delaying tactic, Loki animated the adamantium statues of the founding members and instructs them to attack their flesh and blood counterparts.
Through a combination of the Scarlet Witch's hex power and sheer determination, the Avengers liquify the statues (Wanda destabilizes their molecular structure) which creates a wave of liquid adamantium. They force the wave back toward Loki and trap him in an adamantium prison, sealing off the portal.
Later when things have settled down, Nate Grey, arrives at their front door to warn them that Charles Xavier has gone insane.
This was the first Avengers comic I ever purchased. Primarily because Mark Waid was the writer. The fact it was a milestone issue didn't exactly hurt either. Usually creative teams have a bit more room for these types of stories. Either events leading up to the issue or subsequent issues allow for a larger story. I'm not going to speculate why the previous team was taken off for the final three issues of this series. I have my opinion, but due to sufficient evidence, it will remain just that.
Overall I think the creative team did a great job considering they had to have a milestone event in a single issue. Despite some minor problems, it's an enjoyable read. The use of the adamantium to close the dimensional portal seems to be a stretch. For some reason I have no problem with magic/energy affecting adamantium, but I have minor objections with the reverse. I would assume that metal - even one such as this - can be affected by intangibles, it would not be able to something without a physical presence.
I propose this solution. Since Loki was the link between the dark dimension and Earth, he had to consciously maintain it. Seeing a wave of liquid adamantium coming toward him, Loki lost his concentration and inadvertently closed the portal to focus on more pressing matters. Do I get my No-Prize now?
3.5 webs. If Waid and company had been allowed to use issue 399 as a setup for this story, it would have been even better. However that should not diminish their efforts. For people like myself that aren't 100% up on the Avengers, some of these cameos are not going to make sense as they aren't always identified by direct address or by caption. Readers can easily lump them into "major Avengers' enemies" and continue because they aren't real. I felt it necessary to drop 1/2 web for the adamantium problem. If we allow it to contain magic/energy I think it's no longer an Earthly metal.