So, what does it all mean?
Because it does mean something. After all, it's not like the writers of the Martian Manhunter saga were simply thin-tied tipsy Manhattanites who jotted out his stories in a half hour on the back of a cocktail napkin. LOL, the very idea!
No, these were philosopher-auteurs, crafting J'onn's individual stories and the larger saga that comprises them on the basis of deep insight into the soul, the human condition, and society, who in the space of five full pages could teach us more about ourselves and the world than most modern writers could in three 52-issue maxiseries and three successive company-wide crossovers.
Take, for example, our little Story of the Human Flame.
Joey represents Man's innate sense of our natural limits, born in the knowledge that he is but a speck on a speck floating in the vast sea of space. When we first see Joey, he arrives at Mike's holding a newspaper that has no bearing on the plot. But the newspaper, symbolic of humanity informing itself about the larger world, immediately tells us that Joey is a very much part of society (criminal society, perhaps, but still society). Joey uses the news to understand his small part in the world. Later, when confronted by the awesome elemental force that is J'onn J'onzz, Joey instinctively realizes that opposing him is beyond the purview of man and fears to step beyond such obvious natural limits.
Unlike Joey, Mike strives to set himself beyond society. Whereas Joey clutches to the newspaper to remind him of that he is merely part of a much larger world, Mike lives "in a secluded country cottage", apart from the world, where he crafts devices to augment his natural abilities. His first act is to tell Joey to "stay right there", waiting for him to emerge. Thus Mike sets the boundaries for Joey, reinforcing the message that Joey stays within the limits set upon him by others and the world, while Mike, on the other hand, feels himself immune such limitations, and as if it is his right to step beyond them at will.
Note also that the cottage shows a disheveled window treatment and crooked picture, but a tidy workbench. These are clever artistic details, through which we see that Mike spurns the external courtesies of common society; Mike's cottage is not designed to welcome members of outside society, but is geared toward scientific pursuits to put him farther beyond it. Nature, in the form a bush, grows in full glory outside the cottage window. This is meant to contrast with the view of the inside of the cottage, where Nature has been tamed and roughly enslaved as wood to bar out others (the outer door), and to serve as a mere platform and facilitator of Mike's higher ambitions (as symbolized by the floor and the workbench, respectively). Mike, you see, represents Man's ambition, the will to dominate nature, and to unlock the secrets of God.
Joey is aghast when Mike appears in a suit designed specifically to separate Mike from the outside world. Indeed, Mike is not seen without this suit until the very end of the tale, when he has been denuded of his pretensions toward supra-natural status. On his first appearance, Mike is showing standing the darkness of his own willful ignorance of humanity's proper place in the world, while Joey stands in the harsh light of man's limitations in a larger world. Is it "a space suit", Joey asks? Joey associates the crime suit with the exploration of space, which is not only man's ultimate attempt to ascend the heavens and exceed his natural boundaries but also the very acme of isolation from the regular world. The crime suit represents the history of human science and technology and how our devotion it has threatened to distance us from God, Nature, Society, and a proper understanding of self. Mike replies that with the crime suit, "no cop on earth will be able" to stop him (emphasis added), reinforcing the idea that Mike means to defy the terrestrial limits of man.
Joey then posits J'onn J'onzz as a natural limit Mike cannot exceed. It is clear from this, and everything that follows, that J'onn J'onzz represents Nature, particular as it expresses an intentional higher will to set limits upon Man. In short, the Martian Manhunter is God. This is why his powers are beyond ken, defiant of science, infinite in variety, and incomprehensible (to mere humans) in how and when they are applied. The Martian Manhunter, you'll note, seldom acts directly, instead acting through nature and the surrounding environment to correct and curb the path of wayward man. When Man, aflame with human ambition, forgets his place, God does not shoot him in the leg; instead, he chooses elements of surrounding nature upon which he moves mysteriously so as to dowse this Human Flame. Note, in fact, that when J'onn soaks Mike, it's not with a lake or a rainstorm; instead, he shatters a water tower, a symbol of man's attempts to confine and control the natural elements.
The Human Flame symbolizes humanity's burning ambition to change its place in the world, to be not merely another element of the natural world, but rather its lord and master. Thus, Mike's first act is to attack an armored truck of unknown contents, which clearly symbolizes the attempts of Man (Mike) to utilize technology (the crime suit) to break open the Pandora's box (the armored truck) of nature's secrets (the truck's unknown contents). Joey, you'll note, participates not by aiding the process directly, but by holding the guards at bay, by reminding them of their boundaries and limits, a role consistent with his overall symbolism. Mike, on the other hand, begins his attack by wandering down the middle of the highway, an unequivocal symbol of his willingness to violate ordinary boundaries; "who is that crazy guy in the road", indeed, other than our own foolish ambition, crossing the line and violating the strictures of both society and nature!
God (J'onn J'onzz) impedes Man's attempts to unlock nature's secrets, and with a gust of wind like a natural hurricane blows the truck beyond the overambitious reach of the Human Flame. Nevertheless, poor Mike believes that he can unseat God, that technology, as embodied by the crime suit, will enable him to render God and nature powerless against Man's will.
Such hubris is not easily dampened, even by the downpour of adversity caused by the snapping fingers of God. Self-deceiving Mike/Man does not perceive the hand of God in his adversity, and ascribes the incident only to bad luck. Thus unbowed, he reignites the flame of his ambition and moves from assailing nature itself to violating the boundaries of society, as symbolized by the bank's steel door, behind which lie the arbitrary values that society places on things, here symbolized, of course, by money.
With this endeavor, God does not interfere; our interactions with one another are in our own hands, though God keeps an ever-watchful eye on us. Note, by the way, that in this panel, J'onn describes Mike's assault as employing not "electric bolts", but "artificial lightning", boldly underlining the author's overall intent for us to perceive Mike's crime suit as symbolic of man's attempts to enslave nature to his will, thus mis-appropriating the role of God. Truly, 50 years is barely enough time for us to begin to appreciate the genius that Silver Age writers brought to their craft!
Clearly, at no time are God (J'onn) or Nature in true danger from the machinations of man. With the merest snap of their fingers, we would be gone, reduced to nothingness by the Atom Vision of God or poofed away by the Martian-breath of Mother Nature. But God's goal is not to simply obliterate us; rather it is bring us to a better understanding of ourselves as part of Nature, not as its foes, and to bring us back down to earth when we fly too close to the sun.
In the final confrontation, Man's ambition (Mike) seeks to destroy God (J'onn) through Science (the crime suit), while Man's caution (Joey) looks on, afraid. For a while, God allows us to believe that we have vanquished nature and rendered God non-existent. Man is emboldened by the success of technology in conquering Nature; "God is dead and Man reigns supreme!", Man announces.
But this is clearly folly, and all part of God's plan to return us to right understanding of our place in the world. Because we are blinded by the glare of our own accomplishments, God withdraws from direct interaction with us (as the Biblical Old Testament's Angry God of the Burning Bush gave way to the New Testament's Loving God of Holy Spirit, or the Classical Golden Age of Communion with the Titans gave way to the Bronze Age of Cowering from the Olympians) and retreats into hiding his role within the details of Nature.
God "punishes" us and defeats our ambition by giving us our wish; remaining unseen, he detaches us from nature and places us far above the context of the world and its society.
When they are flown into the upper atmosphere, beyond the comforting context of society and nature, it is Joey (Man's Caution) who announces that they have indeed climbed too high, beyond where Man should go, and the cold that he experiences is both physical and spiritual, as their attempts to set themselves apart from the world has denied them the warmth of society. Suddenly, in the rarefied atmosphere of a universe without meaning, the flame of human ambition falters, and Man seeks only to return to the safety of the known world and the comfort of its contextualizing confines, with the newfound knowledge that to separate oneself from one fellow man is, in fact, to separate oneself from God and from self-understanding.
As Man's Caution chastises his Ambition for its prideful fall, Joey and Mike are brought down to earth and the proper precinct of Man with a harsh realization of their limits and boundaries, as symbolized by their incarceration. "Bah! Still think technology is God's weakness, Michelangelo?"
Meanwhile, J'onn, representing the godly understanding of right arrangement of the world, rushes to return the upturned piece of ground to its proper place within the humble earth. "Sorry I can't stay," God says to Humanity, "but I've got to return this slice of Earth" to its proper place, just as I have now done for you.
I mean, really; the author made it all so clear that it seems hardly necessary to explain it at all.
P.S. The Magical Tudor Barn symbolizes the impermanence and arbitrariness of Man's artificial boundaries between himself and nature. Just in case you were wondering.