The entirety of the clone saga streches well over 100 issues (though not all of them have much to do with the clone saga per se). TPB's you should read are CLONE GENESIS, which reprints ASM #142-#150. These are the issues from the mid 1970's that first introduced the Gwen Clone and Ben Reilly (not yet named).
Also seek out REVELATIONS, which reprints Spectacular #240, Sensational #11, ASM #418, and Spider-Man #75. These are the four issues that ended the clone saga. They told you who was a clone, who was real, who was behind it all, who would live, and who would die.
Finally, you might want to get THE LOST YEARS, which tells a bit about what Ben and Kaine were doing between ASM #150 and the clone saga. Essential issues I would suggest are Spectacular #226, #229, Amazing #400, Scarlet Spider Unlimited #1, Sensational Spider-Man #1, Web of Spider-Man #117, 118, and The Osborn Journal #1.
Spidey runs into Ben (his clone) at the hospital where Aunt May is staying {WEB#117}. He's quite shocked as he (and the readers) believed his clone had died five years ago Marvel Time. Pete, having had a tough time of late, starts fighting {ibid.}. Ben knocks Pete out and makes a hasty retreat {ibid.}. Before he has much time to mull this over, Spidey heads to Ravencroft, an asylum that houses many of his foes, where Judas Traveller and Scrier have taken over {ibid.}. They capture Spidey {ASM#394} but Ben comes to his rescue {SM#51}, seemingly dying at the end {SPEC#217}. Pete goes on to fight Puma (ASM#395,SPEC#218}, get poisoned by the Owl {ASM#396,SPEC#219}, team up with DD {ibid.}, and finds out MJ is pregnant {SPEC#220}. Meanwhile, unbeknownst to Pete, Ben, having survived, makes himself a new costume {WEB#118}, gets dubbed the "Scarlet Spider" by the press {ibid.}, then tackles and beats Venom {SM#52,WEB#119,SM#53}. Ben's presence causes a new character called Kaine to show up who inexplicably has a great hatred for Ben and a desire to protect Peter {WEB#119}. Doc Ock saves Pete from the aforementioned poison , but gets killed by Kaine {ASM#397,SPEC#220,ASM#398,SPEC#221}. Kraven's son the Grim Hunter tackles Ben but gets killed by Kaine {WEB#120,SM#54,WEB#121,SM#55}. Soon, both Pete and Ben experience a kind of "calling" that leads them both to what turns out to be the Jackal's hideout {WEB#122}. He's been "incubating" himself all these years, and begins to taunt Pete and Ben with the possibility of both of them being clones {ASM#399}. He even shows them a new Gwen Stacy clone that melts fairly quickly {SM#56}. Meanwhile, a third Peter Parker has been awakened in the Jackal's lair. This one can't remember much and starts wandering {SPEC#222}. After a battle, Pete and Ben subdue the Jackal and haul him to prison {WEB#123}. Pete gets called to the hospital where Aunt May has revived {ASM#400}. After taking her home, Aunt May reveals to Pete that she has known for years that he was Spider-Man (she prob. found out in ASM # 200), and that she's proud of him {ibid.}. Soon she passes on {ibid.}. Ben, having no more reason to stick around, tells Pete he's leaving forever {ibid.}. Before Ben can skip town, however, Pete is arrested in connection with a murder years ago in Utah. He's sent to jail while awaiting trial {SM#57}. Ben, feeling responsible, goes to the jail and takes Pete's place, giving Pete his Scarlet Spider outfit {SPEC#224}. Pete then sets out to prove his innocence. It turns out that Kaine, who is yet another clone of Pete's {SM#60} (the first Parker-clone Warren ever made), is responsible for the Utah killing {LOST YEARS#1-4}. Rather than see Pete go to jail, Kaine admits to the murder and is taken to prison {SPEC#226}. Pete's name is cleared. Ben and Pete now have time to devote to finding out who the original is {ibid.}. With the help of Ben's friend Seward, tests reveal that Ben is the original {ibid.}. Pete goes batty, hits MJ (accidentally) runs off {ibid.} and joins the escaped-from-jail Jackal with the previously mentioned third Peter-clone who has taken on the identity of Spidercide {MAXIMUM CLONAGE ALPHA}. Ben arrives and fight off a bajillion Spidey-clones {SM#61} to get Pete to come to his senses {MAXIMUM CLONAGE OMEGA}. The Jackal, Spidercide, and newly escaped Kaine all die in one fashion or another {ibid.}. Then Pete almost murders MJ due to a post-death command the Jackal had given him {SPEC#228}. He fights and beats the impulse {WEB#129}. Pete decides that with MJ pregnant, it's time for him to retire, so he and MJ move to the west coast {SPEC#229}. Ben remains the Scarlet Spider for a while {SCARLET SPIDER BOOKS}, but soon his reputation is ruined by an impostor, so he takes back the Spidey identity {SEN#0}. Meanwhile, Pete looses his powers in a lab accident {FINAL ADVENTURE#1-4}. Ben goes on to fight a bunch of villains as the new Spider-Man {SEN#1-3,ASM#407-410,SM#64-67,SPEC#230-233}, and soon Pete and MJ move back to New York. Ben's friend Seward is kidnapped by a mysterious person, and doubt is again raised as to who the clone is {ASM#412}. Pete seemingly dies from some ailment {SPEC#237}, but it turns out that it's just his Spider-powers slowly returning. Seward finds out who the big mastermind is and escapes, off to tell Ben and Pete about the rigged test results {SPEC#240}. Before he can find them, he's killed by Gaunt, an agent for the mastermind {ibid.}. A new waitress at the Daily Grind named Alison puts some drug in MJ's food, causing her to go into premature labor (though she was at least 10 months pregnant marvel time) {SEN#11}. MJ is rushed to the hospital where the attending doctor (another agent of the mastermind) tells MJ that the baby was stillborn {ASM#418}. However, Alison wheels something from the delivery room and takes the "contents" to the mastermind - Norman Osborn (who was dead, but got better) {ibid.}. When Pete gets to the hospital, the doctor drugs him and takes him to Norman {SM#75}. Norman tells Pete that he's the original, not a clone {ibid.}. In a big battle, Norman seemingly dies again, and Ben dies, disintegrating afterwards {ibid.}. Pete finally gets to MJ and they mourn over the baby and Ben for a couple of panels {ibid.}.
The End.
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