I have a 99 windstar that won't start the battery alternator and starter all work but the anti theft thing won't let it turn over what do I do

bypass the starter motor, see the diagrams attached. You will have a new view vision with this.
God bless you

I looked at your security system, it is starter motor disable and fuel injectors. You can usually get the starter crank, but, if it is the security system, it still won't start because of fuel injectors. I don't know any way to bypass security system. You can check for applicable trouble codes, if there are any?

check whether your vehicle is equipped with any immobilizer -anti theft system- as these systems are the one which could cause these unexpected situations.

Try checking the oil, the low oil sensor will disable the ignition

If you have power it would not be an alternator problem unless its not charging the battery and the battery is dead or too weak to turn the starter.
You may have a VATS (Vehicle Anti Theft System) Pass KeyII at fault. Is there a Security light on in the dash?
You may want to start by testing the small wire (S Terminal) at the starter. Hook a test light to it and turn the key to start. If the light comes on then its a bad starter/solenoid. No light then its the ignition switch, any anti theft device (if you have an alarm that disables or is in any way connected to the starting system i.e. remote start, that could very well be the problem) or wiring.

GM vehicles are notorious for failing anti theft systems. When they fail, it turns off the starter to prevent theft even tho nobody is stealing the vehicle. Look at this link. Explains the problem and depending on the year, **** offer a solution http://vatspasslockpasskeysecurityhelp.yolasite.com/

baterr ywas dead changed it-new battery worked-discharged once air turned on-put in 2nd bateer yseems fimne as long as you don't turn on the air-if you do there is a clicking inside radioconsole and discharges battery

Without more info I am going to throw a few things at you, please disregard what does not apply.
Dead or low battery
Bad starter
Bad solinoid
corrosion on the battery
bad connection to the starter
Not all the way in park
Try placing in neutral to start
Bad ignition switch
Anti-theft system activated, lock and unlock door with key
These are not in any specific order
Hope something helps

have you tried disconnecting the battery for 15 -- 30 minutes, it may allow the anti-theft device to reset....

My 2000 cavalier has done this for 6 months. You take your key out then open your door, wait ten minutes and the system resets itself and the car will start-annoying you bet!!!