Kingpin used Fisktronics to illegally sell classified defense plans. However, the feds were on to Kingpin's scheme so Alistair Smythe came up with a plan to frame someone to get the feds off their trail.
Wilson Fisk hired Peter Parker as a diagnostic analyst for the Fisktronics computers. Peter's job was to take home a computer disc which would point out possible errors in the Fisktronics computers.
Peter took home one of these discs. However, Richard Fisk replaced the diagnostic disc with one that contained classified defense plans. Richard then had a corrupt federal agent named Susan Choi arrest Peter for stealing classified secrets and selling them.
Peter later escaped prison and went to Fisktronics as Spider-Man to find evidence to prove he was innocent. Spider-Man found the information he needed on a computer and downloaded it to a disc. However, Daredevil arrived at Fisktronics and fought Spider-Man because he believed he was helping Richard Fisk frame Peter Parker (in reality it was the Chameleon disguised as Spider-Man that was helping Richard Fisk).
While Spider-Man and Daredevil fought some men working for Kingpin detonated a bomb which destroyed the Fisktronics building. They did this to destroy any evidence that could be used to incriminate Kingpin.
However, Matt Murdock later used the computer files Spider-Man downloaded to convict Richard Fisk of treason.