Songfacts®:

• Dream Theater drummer Mike Portnoy was very close to his father Howard, who died of cancer in 2008 and was the subject of their song "The Best of Times," but that's not what this song is about. Portnoy wrote, in response to a question on his website, that if you combine a word from the line before the instrumental break ("Don't cross the crooked step") and a word from the title, you know who the song is about. Thus, we can ascertain it's about his stepfather.
• Mike Portnoy has some harsh words for his stepfather in this song, hinting at a betrayal:
  
  You took advantage of an outreached hand
  And twisted it to meet your every need
  
  "I've never been good at writing love songs, so i decided to write a HATE song," Portnoy explained.
  
  Portnoy eventually reconciled with his stepdad, posting, "We now have a great relationship and do not look back at the negative years (including that song)."
• This song runs 10:14, one of five songs on the Train Of Thought album that's over 10 minutes long. Dream Theater is a prog metal band, but the album is far more metal than prog, with a clear Metallica influence. On the band's previous tour, they sometimes covered Metallica's Master Of Puppets from start to finish.
• Dream Theater often works clips from movies into their songs; on "Honor Thy Father" there's a long rip of them starting at the 5:18 mark. Most of them - the parts about regret - come from the 1999 movie Magnolia. Clips from Ordinary People (1980), At Close Range (1986), and The Royal Tenenbaums (2001) also appear.