Helms had incorrectly installed a gas heater in a house, resulting in a leak that killed the entire family living there.
Pembleton was the primary investigator and key prosecution witness for the case against Helms, so when he is released from prison, he immediately seeks revenge against the detective.
Helms explains to Danny that his plan is to repeatedly tamper with the evidence at the crime scene in hopes that the investigation will eventually become hopelessly confused and publicly humiliate Pembleton.
According to the DVD commentary by director/producer Barry Levinson, NBC was on the fence about whether to renew Homicide for a fourth season; the show was earning critical acclaim, but struggling in the ratings.
Levinson claims that the network led him to believe that the show would be cancelled, and yet failed to give him a definitive answer.
Levinson's decision to give the show's acclaimed regular characters minimal screen time was an act of defiance aimed at the network.