这部拍摄于1989年版的《变蝇人2》是1986年版《变蝇人》的续集,影片承接第一集母亲维尼卡怀上赛斯孩子的伏笔,当她产下一枚蝇蛹时被当场吓死。当局的科研机关巴托工业园收养了苍蝇之子马丁·布朗多(艾瑞克·斯托罗兹 Eric Stoltz饰),由巴托工业的老总巴托先生(约翰·盖兹 John Getz饰)抚养。巴托先生密切监视着马丁的一举一动,表面上把马丁视如己出,实则却把他当作研究对象,暗地里用摄像机记录下他所有的生活过程,让马丁研究他父亲生前的时空传送装置。马丁看上去英俊帅气,无异于常人,除了的惊人的生长速度和超人的天资才能。不久,马丁就与美丽的贝斯·洛根(达芙妮·祖尼加 Daphne Zuniga饰)坠入爱河。可隐藏在马丁体内的变异染色体突然苏醒,等待马丁的是变成下一个“苍蝇人”的恐怖噩耗。
年轻的科学家塞斯(杰夫•高布伦 Jeff Goldblum 饰)刚刚发明一台能传送物体的“电动传送机”,这台机器能将物体分解,传送完成后再自动合成还原。兴奋不已的塞斯决定亲自体验一下电动传送,于是,他进入了传送仓。不幸的是,一只苍蝇这时也飞进了传送仓,于是,在机器将分解 后的塞斯的分子再合成时,将苍蝇的分子也合成到了塞斯的体内。塞斯成了拥有一半苍蝇基因的蝇人。
起初,塞斯的身体就像蜘蛛侠一样变得强壮和精力旺盛,他的女友维罗尼卡(吉娜•戴维斯 Geena Davis 饰)根本不相信男友的鬼话。但是,随着塞斯的身体迅速的渐渐老去,身体开始长毛,牙齿脱落,浑身冒浆,维罗尼卡渐渐接受了这个事实。她并没有遗弃男友,而是和他一起平静的接受了这个事实,即使他变得血肉模糊,她还是和他一起相拥而眠。
1934, America. The Dustbowl. A fugitive named Ben Hawkins finds refuge within a traveling carnival comprised of a tarot card reader and her catatonic/telekinetic mother, a blind mentalist, a bearded lady, and conjoined twins, amongst others. The carnival is owned by the mysterious and unseen Management, who has designs on the young Hawkins, for the boy is concealing an untapped gift: he can heal the lame and raise the dead--at a price. Ben also finds himself disturbed by cryptic and prophetic dreams, which he shares with a Methodist preacher in California, Brother Justin Crowe. Brother Justin, convinced by his dreams he is following God's will, has begun to practice his own extraordinary talents, although the preacher's plans increasingly lead to disturbing and tragic consequences. In this "last great age of magic," Ben Hawkins and Justin Crowe are moving toward a great conflict between Good and Evil, although it not yet clear on which sides these men will stand.