The Doctor regards the mind/brain interface as a physical location: part of the architecture of his brain. He says that he is searching for the bridge between the left and the right lobes; but when he gets there, everything goes mystical. The connection between the two brain hemispheres is an invisible bridge across a dark chasm. He says that the chasm represents "the gap between logic and imagination"; that on one side (the logical side, presumably) is the brain, and on the other side, the mind. He says that the mind and the brain are "two things entirely different but part of the same thing". When they cross the bridge, they are in "the land of dreams and fantasy."
Nothing narratively follows from any of this this. A journey through one of the Doctor's dreams could have been quite interesting: but what we actually see is a projection of lots of Greek columns floating through space. The much foreshadowed interface is a corridor exactly like all the other corridors. The virus takes the form of a large bean-bag with a claw. The Doctor and the beanbag engage in the same kind of mutual taunting as the Doctor and the Rutan did last week.
My best guess is that we are dealing with the then-fashionable but now obsolete ideas of the left and right sides of the brain; where Left Brain is linear, fact-based and logical, and the Right brain is imaginative, intuitive and artistic. Brain turns out to mean Left Brain: mind simply means Right Brain. K-9, who uses big words, knows a lot but has no emotion circuits, is a purely Left Brain entity. Leela, who is all instinct and cannot read, is a Right Brain Person. The Virus attacks the Left Brain: K-9 can be infected even though he is not organic: Leela, because she is ruled by the Right side of the brain, is invulnerable. The Mind-Brain Interface is nothing more interesting than "the bridge between the two lobes". The swarm is a physical virus that jumps into the Left Side of the brain through the optic nerve and then moves to the Right side via the bridge. It was never really neotic at all.
"Don't be funny" says the Doctor to Leela.
The Doctor has just used "Hello!" as an exclamation, in the sense of "I am surprised" or "Take a look at this!" Leela replies "Hello" as if he had just greeted her. I don't know if we are supposed to think that Leela is unfamiliar with human idioms, and the Doctor unfairly assumes she is making a weak joke; or if she is actually making a weak joke.
But "Don't be funny" pretty much sums up the story. Everyone is trying, and no-one quite manages it.
When Leela says that the dark abyss between the left and right sides of the brains is "very deep", the Doctor pretends he thinks that she means that his explanation of the mind/body problem is very profound. When an actual electrical impulse zaps past them, he says that it is "just a passing thought". Leela says "I don't know what to think" and "I have no idea", which are, like, ironic things to say inside the Doctor's head. Like a Shakespearian clown, the Doctor seems to see everything as the opportunity for a wearisome pun. I wish I could say "This is because language is breaking down in the mind/body interface" or "The Signifier is kind of like the body, and the Signified is kind of like the soul." I like wordplay. Basil Brush was not above spending a whole season setting up a bad punchline. But merely twisting meanings for its own sake is not funny.
I have said that Tom Baker's Doctor's arrogance is what made him so hugely attractive to naughty boys in nasty schools in the 1970s. I terribly fear that this just-passing-for-comedy crosstalk between the Doctor and Leela is what my 12 year old self would have thought was smart. Repeating yourself. Deliberately taking colloquial speech literally. Using unnecessarily big words. I don't know if we picked it up from Tom Baker, or if Tom Baker channelled his inner pre-adolescent. It's what Miss Griffiths would have called back-talking. He thinks he's the class comedian. "I know this brain like the back of my hand. What do you know about brains any way? I'll get excited if I want to it's my brain. Oh you want to know something about brains? I'll tell you anyway...." One feels he needs a slap. Miss Griffiths would have given him one.
It turns out that the Bean Bag wanted the Doctor to confront him in the mind body interface. The Doctor has fallen for his stratagem. If anyone were still paying attention this would feel like a terrible cop-out. A reverse deus ex machina. The good guy has spent two episodes doing what the bad guy wanted him to do; making the last fortnight seem like a bit of a waste of time.
They let us go. It's the only explanation for the ease of our escape.
Quite what the Bean Bag's stratagem was isn't entirely clear, but the Doctor totally fell for it. I suppose it thought "What I would really like is to be a giant Prawn in the macrocosmic world. But the only thing that can possibly make small things big is the dematerialisation circuit of a TARDIS. So here's the plan. I shall hang about in space for a billion years: a TARDIS is bound to come past eventually. When that happens, I shall mind control the occupant, because then he is absolutely certain to travel to the asteroid belt, clone himself, miniaturise himself, inject himself into his own blood stream, and confront me in the corridor where the left brain neotically meets the right brain. Then I will stall him for half an episode and at the exact moment he is about to dissolve, I will emerge through the tear duct, and they will think it is the Doctor and turn the embiggening ray on me, and I will turn into a Prawn and conquer the universe!"
It's not the daftest plan a supervillain has ever come up with but it does seem a little on the optimistic side.
The microscopic Leela and Doctor melt into air, thin air, leaving not a rack behind, unless you count the Doctor's scarf and Leela's loincloth and dagger. This is one of many dozens of things which makes no sense: if the Doctor and Leela are clones then surely all their clothing and possessions should survive the time limit? But if they are 3D photos then shouldn't their clothes and personal effects also turn into pumpkins at the stroke of midnight? The camera lingers on Leela's dagger, as if this is of special significance.
Once again, the plot wriggles. For three episode, we have been told that Leela is immune to the virus because she is stupid, instinctive, a hunter -- in short a right-brained person. But when her clone dissolves inside the Doctor, she somehow transfers her immunity to him. And by taking samples of the Doctor's tissue and doing Science on it, the Doctor and Marius can create an anti-spawn-vaccine. In about five minutes. Even AstraZeneka would be impressed.
The virus was never neotic. Leela's immunity never had anything to do with her savageness. The blokes leapt to the conclusion that she was immune because she was stupid, but actually she just happened to have some Virus Repellent Leela Spray in her blood.
Except -- except -- except...
In the final episode, the Intellect / Emotion duality is played out, very unsubtly, in the macrocosmic world. The Prawn is flying back to Titan in a spaceship, where he hopes to hatch an army of giant viruses in order to conquer all of time and space. The Doctor and Marius are trying to breed antibodies from the Doctor's blood. Leela asks why they don't just blow them up. Then she points out that the Doctor is meant to be a pacifist, but he is okay with using antibodies to wipe out a whole alien race. Then she asks why they don't just blow them up. They nip back to Titan in the TARDIS with a plan to introduce the antibodies into the virus breeding tanks. Leela still says they should blow them up. The Doctor confronts the Swarm and carelessly loses the phials of anti-bodies. Leela says it is possible to kill swarm-infected humans by knifing them in the neck. The Doctor doesn't think this is a very good idea. So instead, he blows them up.
The episode has set up a conflict between intellect represented by the Doctor, and action, represented by Leela. ("Do you think that is a good idea?" asks Leela, when the Doctor tells her to use her intelligence.) But in the end, the Doctor's intelligent approach fails, and nuking the site from orbit turns out to be the best solution. Leela's instinct does indeed win the day. There is quite a nice special effect of the base blowing up, but truly, wiring the door to the breeding colony to explode doesn't feel like a very satisfactory conclusion.
Some Doctor Who stories (the Web Planet?) have primitive, even ludicrous, special effects, but succeed because of their strength of their ideas, or their characterisation. And some Doctor Who (Remembrance of the Daleks?) make little sense, but carry us along with shiny monsters, arresting cliffhangers, and fun characters. The Invisible Enemy is in neither category. Some people have tried to defend it by saying that it is simply too ambitious: BBC special effects simply couldn't run to giant virii and journeys to the centre of the cerebellum. But better special effects would not have helped a story which doesn't seem to have been thought through; which doesn't seem to be interested in it's own world or it's own plot. For almost the first time, a Doctor Who story fails on every level: and Tom Baker is not enjoying himself enough, or being given interesting enough material, to save the day.
In the final seconds, K-9 becomes a companion. It is quite obvious to even the least critical viewer that there is no way he can get through the TARDIS door, but he does so anyway. The Doctor does not yet think of K-9 as a person, although Leela does. Marius makes a weak joke about K-9 shitting on the floor. Leela says "please can we keep him, please" like a schoolgirl with a puppy.
If you want to blame someone for the demise of Doctor Who, don't blame Mary Whitehouse, Michael Grade or Colin Baker: blame K-9. K-9 may have appealed greatly to eleven-year-old-me, but he embodied the fact that Doctor Who no longer wanted to be taken seriously. He turned the Doctor into a stooge in his own series. The pacifist Doctor who thought his way out of conflict was now accompanied by a ray gun wielding tank.
But thematically, K-9 had to be in this story. It's a story in which Left Brain Doctor wins the day by giving way to Right Brain Leela; in which the Doctor's brain turns out to be much less exciting than it should have been. So of course there is an artificial intelligence as well. K-9 is there to be the third point in the triangle. K-9 has no brain, but clearly thinks. Leela has a brain, but usually doesn't. The Doctor has a Mind full of fantasy and imagination; K-9 has no Right Brain at all.
Think I am reading too much into the story. Consider this. In the final seconds, K-9 shows that whatever the Doctor thinks, he/it is capable of acting under his/its own agency. He/it decide for himself/itself what he/it is going to do.
He has, says Marius, made up his own mind.