This three issue limited series recounts one of Ben Reilly's "lost" adventures that took place during his roughly 5 year long period of exile between his presumed death in Amazing Spider-Man #149 and his return to New York in Web of Spider-Man #116. It is a murder that occurred in this story that would later get Peter arrested in Amazing Spider-Man #400. This story is meant to be read after "The Trial of Peter Parker" crossover since Kaine's identity (first revealed in that storyline) is mentioned in Lost Years which is a story narrated with knowledge of that "present time" in the Spidey comics. Otherwise you don't need to read any clone saga issues as Lost Years is a self contained story.
If you want to read Ben's story from the beginning then start with the backup story "The Double" in the flipbook editions of the "Power & Responsibility" crossover and then the three part backup story titled "The Parker Legacy" which appeared in Amazing Spider-Man #400, Spider-Man #57 and Spectacular Spider-Man #223 before you read Lost Years. Alternatively you can read Lost Years #0 which reprints all those stories. Again not absolutely necessary but it provides good background for this story.
Lost Years takes place about three years into Ben's exile. Believing himself to be a clone he's a lone nomad who reluctantly helps people from time to time during his wanderings. Unbeknown to Ben, Kaine has been shadowing his trail wishing only to see him suffer.
Kennedy is ordered by Tannen to kill Ben but she doesn't want to do it in front of Raven's son. Tannen instructs Jimmy to take the kid away. Kaine having witnessed Kennedy's duplicity feels betrayed. He crashes back into the warehouse intent on killing Kennedy. Ben temporarily stops him by smashing a crate on his head allowing Kennedy and Tannen to escape in his car leaving Jimmy to fend for himself with kid. Ben knocks out Jimmy and brings the child back to a grateful Detective Raven.
Ben returns to Janine's place exhausted and falls asleep on her bed. He awakes and Janine asks him what happened. Ben doesn't want to explain but notices her bags are packed. Janine was going to leave without telling him and he asks her why. She also doesn't want to explain and proceeds to leave. Ben tells her he loves her and promises to tell her everything but that it has to go both ways. Janine confesses that her real name is Elizabeth Tyne and that she is a murderer. She shot her father who had sexually abused her when she was young and went on the run. Ben reveals that's he's a clone of Spider-Man and takes her along for some rooftop hopping to prove it. For a moment Ben is unsure of how she feels until she asks why he's standing there like a jerk. They leave together on Ben's motorcycle and head out of town.
Kaine has tracked down Kennedy and Tannen to a bar. Tannen is revealed to be Vincent's twin brother Paul from out of town. He blames Kennedy for the screwup and aims his gun at her. Kaine kills Tannen and Kennedy pulls her gun out on him. He asks her why she would ally herself with the Tannens. She responds that they are the darkness and that in the end the darkness always wins. She walks away leaving a saddened Kaine.
Kennedy arrives at Raven's office where he's discovered that Janine Godbe is Elizabeth Tyne and decides to go apprehend her. For reasons unknown to Raven, Kennedy decides to accompany him. They catch up to Ben and Janine making a pit stop at a roadside dinner. Kennedy recognizing Ben tries to shoot him but Ben swats the gun away. He tells Raven & Kennedy that Janine is a good person and to leave them alone.
Ben and Janine drive off into the mountains when Kaine suddenly attacks Ben and a fight ensues. Raven and Kennedy arrive on a lower road and see Kaine and Ben fighting atop a small mountain. Raven and Kennedy race towards the fight but Raven can't keep up since he is out of shape. Ben for the first time in a long time having something, someone to fight for gets the upper hand on Kaine. However, Kennedy arrives and attempts to kill Ben again. Kaine knocks Ben out of the way as Kennedy shoots, and kills her with the mark of Kaine, a disfiguring burn from his finger tips. Raven doesn't see any of this, arriving just after Kaine escapes. Raven points his gun at Ben and tells him not to move. Ben tells him it's not what it looks like and knocks Raven unconscious. The epilogue shows Kaine visiting Kennedy's grave, Raven and his son on a fishing trip and finally Janine holding onto Ben as they ride into the sunset.
The ending is bittersweet which is fitting for this story. Certain plot points don't hold up upon closer scrutiny but in the end this is a character driven story. Ben, Kaine, Raven and Janine are the most well developed. Kennedy not as much. Under all the dirt and rain there are a couple love at first sight subplots with Ben & Janine and Kaine & Kennedy. It's pretty easy to believe Ben and Janine's relationship. Kaine and Kennedy's much less so. However, both relationships create an interesting parallel between Ben and Kaine that highlights their similarities and differences.
Lost Years appears to be a straight-forward crime story but it's used more as a means of psychological character study. If you enjoyed that psychological aspect and the internal monologing then you should also read the superior sequel "Redemption" where the focus is exclusively on Ben, Janine and Kaine.
3.5 webs for the series. It's worth a read even if you're anti-clone and a must-read for Reilly fans.