David Haller, aka Legion, was a powerful mutant and the son of Professor Xavier. In an attempt to make his father's life and legacy much easier, he traveled back in time with the intent of killing Xavier's only major opposition; his former friend and arch-enemy Magneto! However, Xavier sacrificed himself to save Magneto, causing a divergent timeline in which there were no X-Men to stop Apocalypse from taking over the world and having mutants rule supreme. Magneto would eventually come to form the X-Men himself to try and reclaim the world from Apocalypse and honor the memory of his departed friend. With the aid of Bishop, stranded in this new timeline with memories of how things were supposed to be, Magneto and his followers defeated Apocalypse and set things in motion to restore the timeline to its proper form. But, that's what really happened...
In another reality, Legion's attack was more massive and gave the public their first and horrifying glimpse into the world of mutants. Governments captured them and put them into camps, allowing non-mutant heroes to flourish around the world. Ka-Zar in the Savage Land offered refuge to mutants not captured. Apocalypse amassed a huge army and swiftly conquered the world,, creating slaughterhouses to exterminate the remaining humans and breaking the will of other mutants and superhumans to serve him.
In the untouched Savage Land, Nathan Summers is enjoying a nice training session with his parents, Scott Summers and Jean Grey. They have been sure to train him for the day Apocalypse would finally come calling to claim the Savage Land. And that day...is today.
Led by Apocalypse's son Holocaust, the attack comes swift and hard at the hands of Sebastien Shaw, Lady Deathstrike, Cannonball, Banshee, Scarlet Witch and others. Jean and Scott have Sauron whisk Nate away against his will. Sauron took Nate as far as he could before collapsing into the snow of the Antarctic. But they're not alone. Nate readies for a fight but is subdued by the newcomer: Logan! Logan assures Nate he's not with Apocalypse and tells him he was sent to pick him up as the last hope.
Months later, Logan and Nate travel to what was Bleeker Street to meet with other resistance fighters in the former home of Dr. Strange, sorcerer supreme. There, Captain America (armed with both his shield and Thor's hammer) and Brother Voodoo, Strange's predecessor since his death, explain to him the situation and why the world is like it is. Nate explains that his father gouged his eyes out to avoid capture by the police so he has no desire to save humanity, but to destroy Apocalypse he'll do whatever it takes.
After months of training, the Defenders have become a formidable fighting unit, with the addition of Ben Grimm aka the Thing, Brian Braddock aka Captain Britain in a suit of Iron Man armor, Colossus, and Owen Wilson aka the Molecule Man. They show their effectiveness by taking out a couple of scouts that have come too close to their base. Owen is a bit insecure about fighting, but Nate removes those blocks and allows Owen to decimate the scouts. Cap, of course, chastises his actions but Logan backs Nate up. Voodoo talks to Nate where Nate suggests he uses the Eye of Agamotto to guide him back to the anomaly and fix things, but Voodoo says he has resisted the urge in order to follow the plan laid out by Strange. The attack goes as planned the next day.
The Defenders approach Apocalypse's tower, and Thing sees that they're on Yancy Street. This causes him to lament about the Fantastic Four's refusal to become Apocalypse's horsemen, and how Reed and Sue would still be alive if they let it happen. Cap reassures his ally and tells him to use their memory in the fight. That's when Logan smells something familiar in the black gunk crawling up his boots. Britain takes to the air to investigate, but Cap calls him back down. Before he can go, dozens of Spider-Men emerge from the gunk in his black costume look. Nate informs the others that they're clones of Spidey with limited consciousness. Cap orders lethal force on them, citing they're not Peter.
But they were just the distraction, allowing Holocaust to strike! Voodoo tries to hold him back in vain and Nate can't penetrate his mind. Cap manages to rock him with his hammer, however. Nate tells Voodoo they need to enter Dormammu's realm to get around Holocaust because they can't beat him, but Voodoo insists it's a bad idea. Britain takes a shot at Holocaust, but ends up entangled in the clone mess. Thing follows up with a left hook, fracturing his armor while Colossus and Logan execute a fastball special to free Britain. Cap calls down a lightning storm to deal with the clones while Thing and Holocaust continue their dance. However, Holocaust soon vaporizes Thing. Colossus sets out to avenge his comrade, but meets with the same fate. This persuades Voodoo to open the portal and let them into Dormammu's realm.
While navigating the strange environment, Voodoo opens a portal into Apocalypse's lair, but before they can enter Dormammu confronts them. They try to fight, but can't affect him in his own realm. Voodoo orders everyone out while he holds Dormammu back, but Cap is hesitant to leave him behind. Reluctantly, the Defenders leave. Nate lingers just a bit to steal the Eye from Voodoo, causing him to become vulnerable to Dormammu's attack.
In Apocalypse's temple, the Defenders come face-to-face with his horsemen: Hulk, Namor, Storm and Juggernaut. Cap easily takes out Juggie with the hammer and they set their sights on the Hulk. Namor strikes at Logan, but Logan easily skewers himself some seafood, allowing himself to be blasted through by a lightning bolt from Storm. Cap readies to strike at Hulk, but allows himself to be distracted by Nate taken Owen away to fight Apocalypse. This gives Hulk time to rip Britain apart and knock Cap back.
In Apocalypse's chamber, Owen and Nate find the big guy himself, and Owen uses Nate's enhancements to melt Apocalypse from the inside out. The Defenders, finally done with the Horsemen, head in to check on their teammates only to find Nate in Apocalypse's armor. He used Owen to open the Eye and create a portal to the past where he sought to make things right and usher in a new golden age, protected by the armor. Having enough of tyrants, Cap kills him with a bolt. Letting the portal close, Logan and Cap never know that in the process of killing Nate, the bolt inadvertently passes through portal and causes the same events that triggered this Age of Apocalypse to occur in the alternate past the portal actually went to.
The lesson here is one man's best intentions are never best for everyone, and sometimes it's better to work with what you have rather than to try and make it what you believe it should be.
So, as you already guessed, Spidey's only appearance in this is as the mindless clones that "nobody likes" (yet another jab at the Clone Saga). The story had some decent points, but ultimately felt rushed. There was little development of the characters (like how Captain Britain wound up in Iron Man armor, Thing with a cybernetic arm, and Captain America with Thor's hammer), the team, or the world, and instead a head-first thrust into battle after battle. The artwork looked decent in some places, but overall wasn't that appealing. Also, one should note that as What If Featuring X-Men: Deadly Genesis was released the same day, this was the second What If to feature a relative of the summers going crazy and betraying teammates to accomplish a selfish goal, albeit for different motivations.
There are major continuity flubs here. Holocaust was originally Nemesis, son of Apocalypse. He had a human form that was destroyed by Magneto in the original AoA after he killed the Scarlet Witch in a raid on the X-Men compound. As Magneto was killed in the past with Xavier, not only would there be no Scarlet Witch to take part in the attack on the Savage Land (being she is his daughter, unless it was someone with a similar costume), but Nemesis would never be reduced to the energy form that needed the Holocaust armor to keep it together. Also, in a slight nitpick, it's highly unlikely Colossus would manage to have the same costume he had in the original AoA. Also, if you want something to ponder, a lot of the characters featured are at very different places in their histories than their real AoA counterparts were.
3.5 Webs. Rushed, partially poor artwork, and some continuity issues. Otherwise a fair read.