El Capitan and Microsoft Mouse (IntelliPoint) Not Working

To make Intellipoint and the Microsoft Mouse prefpane work in El Capitan, you don't have to disable System Integration Protection (SIP) entirely. You only have to disable one aspect of it. Here are the steps:

1. Restart your Mac.
2. Hold Command-R until the Apple logo appears.
3. From the Utilities menu, select Terminal.
4. In the Terminal window, type this:

csrutil enable --without debug

5. Press Enter/Return. This turns off the part of SIP that will let you run Intellipoint.
6. Type reboot and press Enter/Return to restart your Mac.
7. After the restart you can install Intellipoint. Restart again once you do, and you're set.

UPDATE: dbonneville reported on 10/05/15 that you may need to unplug your mouse and then plug it back in. You may also need to plug it directly into your Mac if you are not already doing that.

If it still doesn't work, follow steps 1-7 again, and this time in step 4, run this command instead:

csrutil disable

If it still doesn't work even after unplugging and replugging your mouse, I would reenable that option with this command:

csrutil enable

I personally only use IntelliPoint for the "IntelliPoint pointer speed" which feels perfect to me, and also the ability to change the wheel button to "Magnify" so I can just press it once to zoom in and then again to zoom back out.

The latest version of USBOverdrive did work for me.  It got the buttons on my Intellimouse Explorer working again.

http://www.senlick.com/html/01.01.html

Install BetterTouchTool and configure the Normal Mice tab to add both buttons. Use Mimic Standard Gestures as the Action and there is a forwards and back option.

I have Sierra v 10.12.1

Microsoft IntelliMouse Optical USB / PS2 Compatible 5-Button

First Download Newest Intellimouse Software

https://www.microsoft.com/accessories/en-sg/d/intellimouse-optical

Install Driver (Security Permissions Most Likely Will Not Let You Open Driver)

Go To System Preferences > Security & Privacy > Bottom Right Click Open

Install Drivers (Mouse Will Still Not Be Detected, That's Okay)

Reboot Will Happen After Install

When Apple Logo Shows Up > Hold Down Command + R

This Will Take You To Safe Boot > Open Terminal

In Terminal Type > csrutil disable

Restart

Now Go To System Preferences > Open Microsoft Mouse

Mouse Should Be Detected.

Once You've Confirmed Mouse Detected > Restart Into Safe Boot Again (Holding Command + R At Apple Logo)

Open Terminal Again > csrutil enable 

Should Be Good To Go! 

I did what you recommended and my mouse still doesn't work correctly.  I cannot set the speed of the mouse.  It doesn't change regardless if I set it to slow or fast.  Is there anything else I can try?