These are the original episode synopses which are listed with the Background Bible document. This document has circulated on the internet and been sold on Ebay.   We can't prove that these are authentic, but it seems reasonable that they could have been first drafts for the episodes.  One copy of this document seen on Ebay had an issue date of April 1986, which would have been around the time season 2 was in planning.

Episode Name: The Cure

MacGyver comes to the aid of a desperate woman, whose father is dying of a rare disease -- for which a cure exists. A major drug company, to enhance its own profits, is withholding the curative medicine illegally.
MacGyver has to penetrate the drug company's well-guarded high-tech laboratories, find irrefutable proof of the cure and along the way, humanize a beautiful woman who has turned herself into a compulsive machine, by dealing with an unsolved problem of his own emotional history.
In the course of the story, our MacGyverisms will include, 1) the use of colorless nail polish to break the "impenetrable" code of a digital vault lock, 2) eluding pursuit by simply switching the "up" and "down" buttons on an automatic elevator, 3) creating a diversion by teaching a lab animal to "speak" via a key-operated vendor, and 4) forcing the revelation of the "cure" by simulting a new, genetically altered disease.

The story involves:

ANNE WILSON, a CPA, and Corporate Manager of Thornton's think-tank, the Tine Corporation. She is the most organized, driven, workaholic human being MacGyver has ever known. She opens and closes the place; she works nights and weekends -- she has no social life, few friends, enjoys neither hobbies nor sports. But MacGyver likes her; he detects a human being somewhere inside that efficient veneer.
So, MacGyver shares Thornton's surprise and concern when Anne Wilson quits. Without warning, without notice, without explanations. Without logic.

Thornton has a clue; her father, her only family, has been ill, he's tried to discuss that area and got himself frozen in his tracks. MacGyver, concerned, takes up the challenge.

He confronts Anne Wilson in her office and demonstrates admiration for her work and her achievement. He breaks through her shell ... and she breaks down. Into wrenching tears. Her work is meaningless -- because her father isn't just ill, he's dying -- and in a way he's being murdered!

The explanation: her father is mortally ill. But Anne, via her professional contacts, has discovered that a major pharamaceutical company has been working on a cure for the disease -- and has found it. And concealed it, engaging in the little known practice of industrializing disease. Because to release a quick cure would destroy the very profitable drug trade they now enjoy. So... she's quit, determined to save her father's life -- even if she has to turn criminal and steal the secret!

MacGyver is a trifle skeptical -- put emotionally hooked; he has to help.

First: are Anne Wilson's suspicions true? The research in question is corporate top-secret; the only way in -- is surreptitiously. MacGyver-style.
Which means entry in broad dayling, clever maneuvers -- interception of secret data -- a chance to encounter DR. HARRISON GRANT, the VP Research -- a man redolent of charm and dishonesty. MacGyver has to pull off a few swifties -- but he gets an answer. Yes. He discovers the company has been pursuing this line, and a month ago clamped down absolute secrecy. They found something. Like a cure.
He brings this confirmation to Anne -- finding her at her father's hospital bedside -- and discovers that vis-`a-vis her father, Anne Wilson becomes an anxious child, a little girl desperately trying to please Daddy. And fated never to succeed. It's revelatory and pathetic. And moving.
MacGyver now understands Anne -- all too clearly. In a personal scene, he reveals that when his father died, he was ten. A boy trying to become a man in desperate circumstances -- and he has always felt that he failed in that attempt; he wasn't able to become his father -- and lived with that impossible task's failure ever since.
Now, MacGyver has an additional motive: to try to help Anne Wilson free herself from her own demands.
If they can confirm the existence of the drug, the FDA will force public admission -- it'll become public.
Together they join, their collective expertise and go into the pharmaceutical company's lab -- slipping past security -- and find themselves in the midst of an incredible high-tech production facility and sudden danger. Because the reason for the self-imposed clampdown a month ago wasn't just the breakthrough on the drug -- it was caused by the methods Dr. Grant used. Dangerous human experimentation. Unethical, probably illegal. Some of the company's employees have been infected; they're trying to cover up a potentially lethal vector.
Using all his skills, MacGyver manages to evade dangers, secure evidence, and -- most important -- give Anne Wilson a measure of reassurance, enough so that she will be able to outgrow some of her demons.

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Click to view the other synopseses:

The Cure (never made)

The Eraser (made, but modified)

Labyrinth (made as The Human Factor)

Blood Money (never made)

Fire Mountain (made as Final Approach, but modified)

The Hard Way (never made)