I see the human conscience like a flight recorder. The "black box"—which is actually orange (Maybe that just makes it easier to find?). It's the first piece of the wreckage that crews will search for when digging through a crash site. It records all the activity that went on during a flight. A flight that never made it to its final destination.
Now, Jesus is the only way to Heaven (the main reason I agree with this theological assertion is because Jesus said it Himself: John 14:6). But upon arrival, I believe that He will take our conscience as the "flight recorder" for our life. Oswald Chambers says that the conscience "attaches itself to the highest that we know". So, when Paul refers to the conscience, as he does many times in his letters (1 Corinthians chapters 8 and 10; 1 Timothy 1:5)--it also features in Acts 23:1, 24:16--it's understood that we as Christians have taken the time to "attach" our conscience with the highest, namely Jesus. Paul wrote that "we have the mind of Christ" (1 Corinthians 2:16). This is true, so develop it. Think along His lines. "Renew" (Romans 12:2) your mind so it's aligned with His. Whatever chemicals (serotonin, dopamine, oxytocin, etc.) that regulate how we feel physiologically, are servants to our will. And as we use our will to think along Jesus' lines, then our brain will follow suit. I don't pretend to know all of the neuroscience behind our conscience and thought processes and feel-good chemicals, and part of me doesn't care. I don't worry about how my food is digested upon finishing lunch. I just know it was delicious. And that I'm grateful. If I had to figure out the digestive process prior to my first-ever meal, I would have died a long time ago.
It's almost as if God, in refusing to allow His creation to outsmart Him, decided to put a "governor" on humans that will keep them in line in spite of them not knowing Him anymore because of sin. Namely our conscience. Jesus says "and as ye would that men should do to you, do ye also to them likewise" (Luke 6:31)--the Golden Rule. And people generally abide by this. Paul wrote in the second chapter of his letter to the Christians in Rome, that those people who didn't get the law (of Moses) do those things contained therein by following their conscience. This is a loose translation. Read Paul's highly nuanced explanation if you have time.
Paul says, in his second letter to the Christians in Corinth (4:2), that he and Timothy had "commend[ed] themselves to every man's conscience in the sight of God." This is a powerful statement, considering that, in order for them to care about appealing to someone else's conscience (making them at ease with what they were bringing to the interaction, i.e. the Gospel), they themselves needed a clear conscience. And that they had aligned their own with the life of Jesus to such a degree that their conscience meshed with those to whom they preached. The Holy Spirit's in and around those interactions, by the way. And with us, in our lives and interactions, this refers to anyone who is doing the best they can, in honesty, with what they know.
Here's the dark side: those whose "black boxes", if I may, are actually black--their conscience having been "seared with a hot iron" (1 Timothy 4:2)--are able through simple mental acrobatics, to act any way you want. They effectively negate the Golden Rule by doing unto others the very opposite of what is right, what is true--in spite of acting "correctly". Paul's words of honesty toward the Corinthians are prefaced with his admission that he had "renounced the hidden things of dishonesty" and had received a "manifestation of the truth". This is what gave him the confidence to appeal to others' conscience: his own was clear.
The Holy Spirit is a person and one of the ways He speaks to us is through our conscience. We need to be sure and heed the "still small voice" (1 Kings 19:12) and not suppress it. I, for one, would like to retain the capacity to feel, thank you very much.
What is the Holy Spirit speaking to you through your own conscience?