You saw her die; now, witness her glorious resurrection!
In Amazing Spider-Man #418, at the end of the Clone Saga, a pregnant Mary Jane apparently miscarried after being poisoned by a woman named Alison Mongrain. It's written by Tom DeFalco and illustrated by Steve Skroce.
In "The Life of Reilly," Glenn Greenberg said that Bob Harras wanted baby May's fate to be left ambiguous, because it "gives hope to the readers who have been waiting for the birth of the baby, it lets them believe that the baby is still out there somewhere, alive, and maybe Peter will find her someday. It'll keep them coming back." However, Harras "didn't want the baby referred to again once the Clone Saga was over."
Flash-forward to 1998. The Spider-books are ending. Amazing Spider-Man and Peter: Parker Spider-Man will be rebooted with new #1s in 1999, while Spectacular Spider-Man and Sensational Spider-Man are to be canceled. The final storylines were "The Gathering of the Five" and "The Final Chapter."
To make a long story short, this is from Alison Mongrain's profile on Spiderfan.org. In a subsequent scheme, Osborn took control of the Daily Bugle by threatening J. Jonah Jameson's family. His purpose was to use the Bugle to exonerate the Osborn name after Bugle reporter Ben Urich wrote a book naming Norman Osborn as the Green Goblin. The normally volatile Jameson was reduced to a lapdog by Osborn, and Robbie Robertson took it upon himself to take the Bugle back from Norman.
His investigations led him to Paris and to Alison Mongrain. Though both Mongrain and Osborn kept their ends of their bargain to each other, neither trusted the other. Alison considered using baby May Parker as blackmail against Osborn, and Norman considered Mongrain to be a loose end. To tie that end up, Norman implanted a painful mind control microchip into the back of the neck of Mark Raxton, aka the Molten Man. The chip would only stop causing pain once Alison was dead.
Once Robbie and Alison returned to New York, they were under constant attack from the Molten Man. Raxton was relentless in his chase, following Mongrain even after he fell into the harbor after battling Spider-Man. Mongrain, believing to be safe, wanted to go to the Parker home to tell Peter an urgent message. The ground beneath her suddenly erupted, as the Molten Man emerged from the sewer. A block of concrete hit Alison in the stomach, badly hurting her. Suddenly realizing that the Molten Man was following the necklace that Osborn had given to Mongrain, Robertson threw it away, where Mark destroyed it.
This is from Amazing Spider-Man #441, the last issue of the series before the reboot. It's written by John Byrne and illustrated by Rafael Kayanan.
Meanwhile Norman, Madame Web, Mattie Franklin, Gregory Herd, and a pawn shop owner named Morris Maxwell participate in the Gathering of the Five, a ceremony in which each person receives one of five "gifts": power, madness, knowledge, immortality, or death. Madame Web recieves death, Mattie Franklin receives knowledge, Gregory Herd receives immortality, and Morris Maxwell receives madness.
This is from Peter Parker: Spider-Man #97. It's written by Howard Mackie and illustrated by John Romita, Jr. The cover is by Byrne.
Norman blows up his henchmen and flies off.
Spidey heads to the aforementioned hunting lodge, where he gets attacked.
After finally managing to hold Norman off...
This is from Spectacular Spider-Man #263, the last issue of the series. It's written by Mackie and illustrated by Luke Ross.
Peter heads to the FF Plaza...
Reed tells Peter that she's definetely human, and not a clone or some other artificial lifeform, but to confirm that she's really May he asks for a sample of her DNA that they know couldn't have been tampered with. Peter finds an old science experiment in his attic that contains a blood smear from Aunt May.
Peter heads to Oscorp and confronts Norman. After battling him, Norman shows him how his DNA bomb works.
As Norman takes him outside, he says he's used his charitable organizations to distribute thousands of the DNA bombs.
Norman beats Peter up some more, telling him that he wants his death to be public and slow. He reveals how he faked Aunt May's death.
Norman unmasks Peter in front of everyone at the Daily Bugle and kills him.
This is from Peter Parker: Spider-Man #98, the last issue of the series. It's by Mackie and Romita.
Yes, it turns out that the gifts weren't what they seemed and that Norman actually received madness, and not power (it's later revealed that Madame Web really received immortality, Mattie Franklin really received power, Gregory Herd really received death, and Morris Maxwell really received knowledge).
A stray pumpkin bomb explodes, causing the Daily Bugle to collapse. Peter is able to hold it up long enough for everyone to get away.
The scene cuts to Peter and MJ in the waiting room.
And how does Aunt May deal with being kidnapped and having her death faked? Here are two scenes from Amazing Spider-Man v2 #1 and #2. Both are written by Mackie and illustrated by Byrne.