The Mitochondrial Disease
Consider Charles Wallace's strange illness in the novel. The symptoms of the illness resemble asthma, often leaving Charles unable to breath correctly. But the disease itself is actually a problem in his very cells, in his mitochondrial farandolae. This symbolic affliction is eventually seen to be the result of extraterrestrial or supernatural attacks by the evil Echthroi. In its context, this illness suggests firstly, that even when a medical explanation for a disease is offered, there still might be a compatible cosmic answer that helps explain, at least in this instance, what the relationship between disease and evil. L'Engle seems to suggest that illness itself might be the consequence of evil forces which are enemies to humans and want to challenge and confuse them.
The illnesses asthmatic nature is also interesting. L'Engle often employs Greek words in her stories, meaning that she might be familiar with the Greek word 'pneuma' for breath, and also for spirit or air. In light of this, another possible interpretation of this symbol is that the evil forces are afflicting Charles Wallace's access to spirit or air, which in the context of L'Engle's Christian, allegorical style, might mean that more importantly than Charles' literal shortness of breath, his illness is an existential frustration, a shortness of spirit. This is well within L'Engle's philosophical camp, since Christianity has likened man's struggle against evil to a disease. This is another way L'Engle evokes interesting ideas about the relationship between the body and the soul, and the relationship between evil and decay or disease in the literal world, ideas which have been explored in Judeo-Christian philosophy for thousands of years.
Supernatural forces
This concept, whether aliens exist, is a wonderful feature of L'Engle's writing style. It's a wonderful question for her literary purposes, to ask the reader to indulge the imagination where dragons and evil baddies exist, just beyond our current perception of reality. A Wind in the Door adds another layer of color to this fantastical element by describing the dragon, alien thing called Proginoskes as having many eyes and many wings, a description that clearly alludes to the Revelation of St. John, which in chapter 4 contains a similar description of the angels John calls 'Seraphim,' from the Hebrew for 'the Burning Ones.' A good argument could be made that the very title of the novel is a reference to this chapter of the Bible, since the chapter begins with John seeing a door in heaven, and he goes there, 'en pneuma,' which means 'in the spirit.' A Wind in the Door could easily be a reference, then, to the act of revelation, or of taking a peek into the mystic, cosmic world beyond our literal reality.
Consider that the aliens that the novel introduces all have Greek names. Proginoskes is the New Testament Greek word for 'Foresight,' or 'Foreknowledge,' which means that the children, through their relationship with this alien dragon thing, are engaged in an act of prophecy, perhaps, a prophecy that teaches them that there is a supernatural enemy (Echthroi means enemies in Greek), and that the evil forces hate the humans are cause them to harbor hate in their minds and souls, and which cause them physical diseases. They also learn that empathy and divine (or extraterrestrial, to be exact) assistance are important weapons in the strange cosmic battle that we experience in non-direct ways in our lives.
The problem of loneliness and intelligent thought
In the novel, Charles Wallace is shown to be experiencing the isolation and frustration that often accompany high levels of intelligence in the lives of young adults. This is not to say that average thinkers don't experience loneliness; it just shows a specific kind of loneliness, loneliness as the product of higher thoughts. The novel answers this concern in two ways: Firstly, it shows Charles Wallace in the act of adventure, next to friends and family (cosmic and natural), and secondly, it shows that the quest toward higher truth can be therapeutic and meaningful.
This first answer is sweetened when Charles is allowed to enjoy cosmic company with an alien who helps the protagonists in their quest. Sure, he might get picked last in PE or something, but he gets to explore the supernatural with his sister and friend, and he is healed from a strange illness in the process. This second aspect is important too. L'Engle shows us that along with Charles frustration, there is a unique affliction that drives him to pursue his fate, despite his loneliness. This type of question is also seen in stories like The Lion, the Witch, and the Wardrobe, or even Alice in Wonderland, and the argument in all cases seems to be that there is something sacred about adventure, even though by its nature, it requires the sacrifice of common things and normal popularity.
This is a strange and beautiful consolation to a problem that everyone endures eventually, and even when a young person grows up and moves beyond school popularity into the 'real world,' the lesson is still applicable. Life will involve the frustrations of loneliness and feeling misunderstood. A Wind in the Door seems to suggest that the cure for those afflictions is that we are not alone in the spirit, and there is adventure to be found in looking for aliens and trying to heal broken aspects of ourselves, just like Charles Wallace makes a friend in some ancient alien dragon and finds healing for his mitochondrial illness.
Mr. Jenkins as a symbol
Mr. Jenkins is a minor character in the story, whose inclusion in the story allows us to explore interpersonal relationships through Meg's perception of him.
Although in reality, Mr. Jenkins isn't particularly intimidating, Meg is seen in the story to perceive him to be some sort of monster with a vendetta against her and her family. In reality, however, it's the Echthroi who are creating false versions of him for her to indulge in. This is a clever ploy! If the enemy can turn the humans against one another, then it becomes harder for the humans to correctly see where the real threat is.
But Meg manages to parse the real from the false, through the employment of empathy. She realizes that the fake versions of Mr. Jenkins are indulgent, meaning that they play into Meg's biases against Mr. Jenkins. The irony here is that Meg is the antagonist of Mr. Jenkins, viewing him in an unfair, enemizing way. But, when she finally learns to see him correctly, she isn't scared of him anymore, and she can continue in her quest.
The Echthroi
The Echthroi are a wonderful example of the forces of evil that make books like L'Engle's so powerful and fun to read. The word Echthroi is a transliteration of the Greek word for enemy, which highlights the proverbial nature that they represent. The author goes almost all the way to just calling them, "The Bad Guys."
So what is the purpose of the Bad Guys? In this story, the enemies are enemies specifically against the extraterrestrial forces of good, specifically by attacking the humans. But, they don't literally attack the characters. Instead, the use clever strategies to confuse or frustrate Charles Wallace, Meg Murry and Calvin O'Keefe.
Their inclusion in the story is a reminder that in the world of A Wind in the Door, there is often more to reality than what we can sense normally. The first step in defeating the Echthroi is by understanding that they exist, and for whatever reason, they are willing to go through the trouble of challenging each human specifically. So for Meg, this means that she has to be careful to not allow resent to fester and grow into hatred. She has to turn to the cosmic forces of love and patience to conquer the Echthroi's unique challenge in her story. For Charles Wallace, it means having to depend on his loved ones who advocate for him to a young farandola. In other words, he has to trust that through the help that Progo represents, and through the love of his sister, he will be healed from his strange disease.
The point is that the forces of evil are clever, and they attack in ways that don't seem obvious, working both against the body and the mind, but through virtuous acts of charity and faith, humans can have victory against them.
