So to recap: Spidey learned about the Kingpin's presence in New York and wanted to do something about it. He managed to infiltrate the Kingpin's quarters and stole his security tapes, finding evidence of Fisk murdering one of his underlings and releasing it to the media. Thus, Kingpin fled the country.
In #47, the Enforcers are roughing up someone who owes Kingpin money. Spider-Man comes, causes trouble and then the police arrive.
#48, Peter is pissed. He got into a fight with his teacher over the Kingpin being able to walk free and was suspended. He was also fired from work for bringing the matter up to Jonah, asking why he was focusing all his time on Spidey when Fisk is a bigger problem. So he decides to take it out on Fisk.
Later, Ben Urich has an interview with Sam Bullit. The anti-Spider-Man issue is brought up, and Ben Urich asks why, with all of the issues New York has, that Bullit would tackle Spider-Man. Bullit says Spider-Man is a symbol for all the havoc caused by vigilantes in costumes, and Urich responds that some of these vigilantes are in fact government employed.
Urich, it turns out, had an extra recorder hidden under his jacket. With Bullit exposed, Jonah has no choice but to grudgingly revoke his support and publish an editorial about Bullit's mob leanings.
#49, the Enforcers decide to rough Jonah up for his disobedience.
Spider-Man, it turns out, was planning on paying Jonah a visit of own to protest Jonah's general douchebaggery. Ergo, he's forced to save Jonah. In the process, the Enforcers get the upper hand on Spidey.
Spidey uppercuts Ox, knocking him out. Jonah grudgingly thanks Spidey. Later on, he rehires Peter and apologizes for his behavior, admitting that he may have been hasty in judging Spider-Man. It's a nice scene and one of Jonah's best moments in either continuity. More incentive to buy the trade.
Anyway, Spidey decides to pay a visit to Fisk.
Prior to this, pretty much all of Spidey's vilains were brought to justice at the end of their arcs. This was the first time that the villain wouldn't be put away so easily, and IMO established Fisk as one of Spidey's best antagonists.
Next: The Black Cat causes trouble for Kingpin, and Elektra gets involved. 'Nuff said!