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What did Finkle want? Why did he go to all of that trouble?
He wanted redemption after being disgraced by missing the kick that cost the Dolphins the game in the 1984 Superbowl. He also wanted vengeance against Marino, who was the one truly at fault (if he’d held the ball properly, Finkle wouldn’t have missed the kick, as evidence by his precision kick through a small opening in the roof of the warehouse; even in high heels). Finkle was disgraced so badly that his house was vandalised and shot; he was presumably beaten (a deleted scene reveals this in the original script) upon returning to his home, and no football team would ever touch him again. He was vehemently hated by all - all because of Marino.
What was Finkle's plan?
Finkle’s plan was to kidnap Dan Marino and Snowflake, to make the Dolphins suffer defeat in the Superbowl when Marino could not be there. Snowflake was kidnapped so that Finkle could say that he caught Dan Marino killing the dolphin, a crime for which he would be jailed and disgraced. Then he would conduct the necessary investigations as a woman, then have his implants removed and get back to being Finkle, who is now redeemed (Marino is crazy, he shouldn’t be believed when he says the laces were out like they were supposed to be). It’s imperative that Finkle keeps up his pretense as a woman around Marino, so as to not arouse suspicions when Marino starts screaming about Lois Einhorn being Ray Finkle.
How was he going to enact his plan?
Finkle needed somebody’s identity. He decided to pick up a hitchhiker with the intention of killing him, as a hitchhiker could be killed away from prying eyes easier than anyone else. After long periods of searching, he eventually stumbled onto Lois Einhorn. While this was not ideal, Finkle killed her and took her identification, and assumed the identity of a woman. Even though it would be easier to assume the identity of a woman, and the fact that being a woman would have many side-benefits that would make the plan much easier, it meant giving up women and forcing him to lead an incredibly difficult and stressful life for a time, but it was worth it to get back at Marino.
After perfectly his makeup skills, female vocals (he found it easier than most, all he had to do was make sure to avoid his male register; not a simple thing that required constant monitoring, but still comparitively easy) and female movements, he began seducing his way to the top of the Miami Police Department, where he would be in a position to manipulate evidence, and never ever be suspected as having anything to do with the crimes he was about to commit.
Before the Superbowl, Finkle would seduce somebody to get the key to the stadium in order to extract the Dolphin.
Did everything go to plan?
The plan was going flawlessly until Ventura showed up.
He caused everyone to think Roger Podacter (the man who Finkle seduced in order to get the stadium key, and later dated to keep up the pretense), was murdered. The plan was to make it look like a suicide.
Infuriated and terrified of Ventura discovering the truth, Finkle ordered his thugs to kill Ace, but he avoided
Ventura later showed up in Finkle’s office and let on that he knew about the whole plan. Some of the things he said made Finkle think Ventura knew about his diguise, causing Finkle to almost have a heart attack. Finkle was able to keep up the pretense however, despite the worry, kissing Ventura to verify that he still thought he was Einhorn.
Terrified and infuriated over Ventura’s persistence, Finkle ordered his thugs to kill Ace, but he avoided them during both their attempts.
Ventura showed up yet again in the warehouse just as the plan was coming fully to fruition. Finkle adapted and thought to set Ventura up as Marino’s accomplice. Finkle became distracted however, after one of the announcers for the Superbowl insulted Finkle to the millions watching the game, on one of the sets Finkle set up to show Marino how badly his team would lose, allowing Ventura to wrestle the gun away from Finkle as he was about to kill him with the intention of saying that Marino killed Ace when he started to get cold feet. Finkle was unable to subdue Ventura before the police came, allowing Ventura to expose his plan. No-one believed Ventura of course, not until he stripped Finkle’s dress away, revealing the penis Finkle kept hidden in the back of his panties, to the entire force that he himself called.
Finkle was presumably arrested for the murder of Podacter and the kidnapping of Snowflake and Marino. It is reasonable to assume that Finkle’s conviction did not go well, after angering the entire force by fooling them into think he was a woman, and tricking them into having homosexual sex.