The System Will Not Save You; The System Cannot See. (John 3:1-15)

The Dissidents Guide to John, Part 4

Mar 26, 2025

Nicodemus and Jesus

In John chapter 3, we’re introduced to a Pharisee named Nicodemus—one of the first religious leaders to engage Jesus after he begins his public ministry. On the surface, it’s a quiet, curious visit. Underneath that, this story is not just about a man who comes to Jesus under the cover of darkness, but about the fundamental difference between two ways of seeing the world—and the subtle, spiritual choice we’re all invited to make.

John’s gospel is offering us more than a biography of Jesus. He’s inviting us to compare the religious systems of his day to our own and ask ourselves some questions like:

~ How do we recognize the presence of God?
~ How do we determine what is spiritual and what is simply cultural?
~ What do we do when our own religious assumptions become obstacles to encountering the divine?

This passage, like much of John’s Gospel, works through tension. Each of the five central ideas in this story comes with a double meaning—one that speaks to the earthly way of thinking, and one that opens a door into something spiritual. And in every case, the two are in conflict. They cannot co-exist.

Jesus and Nicodemus, though only a few feet apart, stand in completely different worlds. The question for the reader is, both then and now: which one are we standing in?

1. Night

“He came to Jesus at night.” — John 3:2

Let’s start with the most obvious symbol John gives us: night.

Yes, it’s literally night—Nicodemus comes under the cover of darkness. But the word nux (greek) can refer not just to the absence of sunlight, but also to spiritual and moral darkness—ignorance, confusion, and disconnection from God. Nicodemus is in the dark. And not just physically, but also spiritually.1

Nicodemus is not some outsider. He’s a respected Pharisee. A member of the Jewish ruling council. A teacher of Israel. And yet he is spiritually darkened, unable to recognize Gods work and presence. That’s John’s point. Religious authority does not equal spiritual awareness. Sometimes it actually gets in the way.

Nicodemus represents more than himself. He embodies the very system that, a generation later, would expel the community behind John’s Gospel. Obviously, the author(s) of John have little trust in institutional religion. and moments like this make it clear that they thought of them as being spiritually unenlightened.

Nicodemus tries to be respectful:

“Rabbi, we know that you are a teacher who has come from God. For no one could perform the signs you are doing if God were not with him.” (V2)

He’s impressed by the miracles; enamored by his gifts. For them, spectacle is how the divine presence is seen. In fact, that’s how he (and by insinuation, the rest of the temple leadership) gauges spiritual authority—by impressing the throngs, influence and audience reach.

For anyone who grew up in our modern age of seeing the church as The Big Show, this mindset may sound familiar. For decades, we have been enamored with trendy, fast-growing churches with massively influential pastors bringing in millions of dollars, expanding across counties and states while pulling in tens of thousands of members. For a while, it felt like something powerful was happening.

We all looked at it and said: “this has to be God. Just look at the fruit.” But we did not mean the fruit of the Spirit, we meant growth and power; it was the fruit of the Empire.

But there were prophets—people like Rachel Held Evans—warning us: “this is empire, not Spirit.” And they were right. In the end, so many have come crashing down, leaving behind a trail of spiritual abuse, toxic masculinity, financial exploitation, and deep trauma.

We are often like Nicodemus. In the dark. Confusing cultural success with divine presence. But Jesus isn’t playing that game. And when Nicodemus tries to engage him on those terms, Jesus shifts the conversation.

2. Born Again / Born From Above

“No one can see the kingdom of God unless they are born again.” — John 3:3

The Greek word Jesus uses—anōthen—is intentionally ambiguous. It can mean “again,” as in a second physical birth. But it also means “from above,” pointing to a spiritual rebirth initiated by God.2

Nicodemus hears the first meaning and misses the second:

“How can someone be born when they are old?”

Jesus responds by pointing toward baptism.

“No one can enter the kingdom of God unless they are born of water and the Spirit.”

It’s a call to transformation—a divine rebirth.

Nicodemus can’t wrap his head around it. He’s still imagining the kingdom as something that can be earned or managed. But Jesus is describing something completely different—new eyes. Eyes that look at the same world, but see a different way.

3. The Wind and the Spirit

“The wind blows wherever it pleases… so it is with everyone born of the Spirit.” — John 3:8

Here, Jesus plays with another double-meaning word: pneuma—which means both “wind” and “spirit.” The Spirit of God, Jesus says, is like the wind—free, uncontrollable, unbound by human systems. You don’t get to manage it. You can only follow where it leads.

For someone like Nicodemus, trained in the art of religious structure, this is deeply unsettling. But that’s exactly the point. We have no control over what God is doing, what God can or cannot do. The way of the Spirit is about letting go. Letting go of control, of hierarchy, of outcomes. It’s about trust, even when the direction doesn’t make sense.

Nicodemus still doesn’t get it. And Jesus responds with a jab:

“You are Israel’s teacher, and you do not understand these things?” (V10)

It’s not just about Nicodemus. It’s about every generation of spiritual leaders who mistake order for faithfulness, and systems for the Spirit. You may be controlling people, but you cannot control the divine.

4. Lifted Up

“Just as Moses lifted up the snake in the wilderness, so the Son of Man must be lifted up.” — John 3:14

This reference is layered. It pulls from a moment in Israel’s wilderness wanderings, where a bronze serpent is lifted up and those who look at it are healed (Numbers 21:4-9). It’s a story about trust—faith that heals in the midst of suffering.

But Jesus uses the word hypsoō—which means both “lifted up” and “exalted.” He’s talking about the cross, something which high status people like Nicodemus view as humiliation. Shame. Failure. But in the eyes of Christ and his kingdom, it is exaltation. It is the path that Jesus takes to become Lord of all. His greatness comes through the cross —not through gold and power, but with vulnerability and sacrifice.

This is why Paul would later write:

“We preach Christ crucified: a scandal to Jews and foolishness to Gentiles.”
— 1 Corinthians 1:23

The scandal was social. The cross was a shameful death. No one wanted to be associated with a crucified messiah, especially the wealthy and influential. But Jesus keeps insisting: this is what real glory looks like. And if that’s true, then it also reshapes how we look at the people our culture “lifts up” to be shamed. The incarcerated. The undocumented immigrant. The gender queer. The poor and homeless. The ones rejected by the powerful. The ones empire puts on a cross.

Jesus is there, not above them, but with them, and lifting them by the hand at his resurrection by the spirit.

5. Eternal Life

“…that everyone who believes may have eternal life in him.” — John 3:15

Eternal Life (zōēn aiōnion) isn’t about later, it’s about a new kind of life. A divine, eternal life that begins now, dwelling in the new Jesus era. A life that sees through Jesus’ eyes, and one that listens with His ears. One that responds to the world not with fear or dominance, but with love, courage, and compassion.

Eternal life is disruptive to those living the temporal life —that is, a life for power, wealth, success, and upward momentum, because it messes with the way things work in a world built on self-preservation.

Those living eternal life force hard choices on the rest of us. They will declare:
“this may hurt your pocketbook but it will help your neighbor!”
”That that may hurt your reputation but will align your soul with the kingdom.”

The choice will always abide because the two worlds—light and dark, empire and kingdom—cannot coexist.

To be a follower of Jesus is to be baptized out of one and into the other. That doesn’t mean we’re perfect, but it means that we are committed to the pursuit of the light. It means repenting when we see the darkness in ourselves. And it means that the Spirit walks with us as we journey towards the Father together.

New Interpreters Bible Commentary, Volume VIII.

Ibid