Why do I keep getting pop-ups that say I have a virus and files from my OS X are missing?

These are scams. Ignore them. Beware of Browser Pop-Up Tech Support, Phishing Scams.

iDevice Safari Phishing Adware Pop-ups

Your device does not have a virus. You can fix this as follows:

1. Kill Safari by double-tapping on the Home button. Locate Safari in the task bar, then slide the Safari mini-page upwards so it vanishes.
2. Tap Settings > Safari > Clear History and Website Data. Next, locate Security section and slide the “Block Pop-Ups” switch to the On position.
3. Press the Home button to return to your Home screen.
4. If this doesn’t help, then reset your device. It won't delete your data. Press and hold down the On/Off button and the Home button until the display turns off and returns with the Apple logo showing.
5. Alternatively, follow these instructions to reset your device: Restart your iPhone, iPad, or iPod touch - Apple Support.

Fixes for Adware and Pop-ups

1. Malwarebytes

2. DetectX 2.11

3. Remove adware that displays pop-up ads and graphics on your Mac

4. Stop pop-up ads and adware in Safari - Apple Support

[Please ignore remarks such as “Don't use any kind of "anti-virus" or "anti-malware" product on a Mac.“ Such remonstrations are an exaggeration. They may be needed in some situations, but need not be installed or used for all circumstances. Furthermore, adware removal programs make the job of removal much easier. They require no permanent installation to remove adware or other types of malware. They do no damage, and they don’t make you more vulnerable to attack.]

Fixing Safari from Pop-ups

[The following comes from user stevejobsfan0123. I have made minor changes to adapt to this presentation.]

Fix Some Browser Pop-ups That Take Over Safari

Common pop-ups include a message saying the government has seized your computer and you must pay to have it released (often called "Moneypak"), or a phony message saying that your computer has been infected, and you need to call a tech support number (sometimes claiming to be Apple) to get it resolved. First, understand that these pop-ups are not caused by a virus and your computer has not been affected. This "hijack" is limited to your web browser. Also understand that these messages are scams, so do not pay any money, call the listed number, or provide any personal information. This article will outline the solution to dismiss the pop-up.

Quit Safari

Usually, these pop-ups will not go away by either clicking "OK" or "Cancel." Furthermore, several menus in the menu bar may become disabled and show in gray, including the option to quit Safari. You will likely have to force quit Safari. To do this, press Command + option + esc, select Safari, and press Force Quit.

Relaunch Safari

If you relaunch Safari, the page will reopen. To prevent this from happening, hold down the 'Shift' key while opening Safari. This will prevent windows from the last time Safari was running from reopening.

This will not work in all cases. The shift key must be held at the right time, and in some cases, even if done correctly, the window reappears. In these circumstances, after force quitting Safari, turn off Wi-Fi or disconnect Ethernet, depending on how you connect to the Internet. Then relaunch Safari normally. It will try to reload the malicious webpage, but without a connection, it won't be able to. Navigate away from that page by entering a different URL, i.e. www.apple.com, and trying to load it. Now you can reconnect to the Internet, and the page you entered will appear rather than the malicious one.

[Permission to use part or all of the above has been granted by Kappy, exclusively, to theratter.]

It's a scam. Do not call!

Quit Safari from the Apple > Force Quit menu. Relaunch Safari from the Dock icon while holding down the Shift key.

Reading this might also be helpful.

Mac Malware Guide: How do I protect myself? http://www.thesafemac.com/mmg-defense/

Don't use any kind of "anti-virus" or "anti-malware" product on a Mac. There is never a need for it, and relying on it for protection makes you more vulnerable to attack, not less.

Your problem is most likely not caused by malware. It's a Web scam that only affects the browser, and only temporarily. There are several ways to recover.

1. If you're running Safari 9.1 or later, just close the window or tab. Then go to Step 6.

2. If you're running an older version of Safari, the easiest thing to do is to force quit the browser. Relaunch it by holding down the shift key and clicking its icon in the Dock, the LaunchPad, or the Applications folder.

You will lose the state of other open tabs and windows. Either Step 3, Step 4, or Step 5 may enable you to keep that state information. If those steps don't work, fall back to Step 2.

3. If there is a checkbox in the popup marked

Don't show more alerts from this web page

check it, then close the popup.

4. Press the key combination command-W to close the tab or window. A huge box will pop up. Press the return key and both the box and the page may close. If that doesn't happen, press and hold command-W. You may hear repeating alert sounds. While holding the keys, click the OK button in the popup. A different popup may appear, which you can cancel out of as usual.

5. From the Safari menu bar, select

Safari ▹ Preferences... ▹ Security

and uncheck the box marked Enable JavaScript.

6. After closing the malicious page, select from the menu bar

Safari ▹ Preferences... ▹ Privacy ▹ Remove All Website Data

to get rid of any cookies or other data left by the server. Open the Downloads folder and delete anything you don't recognize.