Once Mail is launched got to Mail>Preferences>Accounts.This will stop Mail trying to download mail on launch. Turn Wi-Fi off before launching Mail, disconnect your Mac from the Internet.(Though it seems odd a Unix-based OS has a problem handling the task). If your Mail has been crashing on launch, you can sometimes prevent this behavior by taking control of your accounts and making them turn on one at a time, instead of all at once. Then write to the developer and ask for help. If it does, then re-enable your extensions one at a time so you can identify which one is causing your problem. If you are using any third-party Mail extensions and you’re having problems using the app, it’s a really good idea to disable your extensions and relaunch the application. You should repeat the process for each of your troublesome accounts. If it is unchecked, check it and relaunch Mail if it's checked, then uncheck it, quit and relaunch Mail, reenable it and then quit and relaunch Mail once again.Look at the list and at the top of the list you’ll see the ‘Automatically detect and maintain account settings’ tick box.If one of your accounts seems to be misbehaving (it may not be sending email, seem inactive or in other ways seem faulty), launch Mail Preferences and select the account in the Accounts tab, then click on the ‘Advanced’ tab. This fix seemed to help when OS 10.10.4 shipped earlier this year, so it seems worth trying in OS X El Capitan. Set the ‘Outgoing Mail Server’ section to the right to iCloud.Launch Mail and open Preferences>Accounts.Once this process completes, click on the box to turn Mail back on, and close System Preferences.

Open System Preferences>iCloud and unclick the checkbox beside Mail to disable it.If you can’t send email using your iCloud account after upgrading to El Capitan then following these steps may help:

Where are apple mail preferences stored