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There are 2 types of options, that are very different from each other: minor league options, and contract options.
Minor league options are what are referred to in the settings page. They are essentially the number of years that you can send a player to the minors, once they have been placed on the 40-man roster. So if a player has 3 options, they can basically be sent down to the minors this year, next year, and the year after that, but after that point, you're not allowed to send them to the farm anymore without them clearing waivers or being DFA-ed.
Contract options are totally separate, and are simple decisions on whether to bring back players at a certain salary.
As for the players retiring, I always forget what options are allowed in random debut modes, but I know in historical mode, you can either have players retire according to history, or have them retire according to the game development engine. If you have the game engine control them, then yeah, some guys who had one or two down years later before a late career blip might decide to retire, since they never "look ahead" to see how they will be in the future.
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