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I think my rooted cyanongenmod phone was hacked. What can I do to start fresh again? I already did a factory reset but after 1 month the phone started acting weird again (battery time dropped significantly, home screen mysteriously changes, unexpected reboots of the phone and the other day I saw that my phone was rebooting and installing something that looked weird at 3 am).

My phone is a Samsung Galaxy Nexus I9250 if that matters.

Should I format SD card also?

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    Flash the whole firmware. That's the only option now. Although it would be useful to us if you detail more about the events such as what the phone was installing at 3AM or what kind of mysterious changes did you notice at home screen? Please note, did you monitor network activity on your device? It is very important to conclude that the device is hacked. – Firelord Sep 23 '15 at 12:47
  • Thank you @Firelord I will investigate how to flash the whole firmware. At 3 AM I saw an android logo with text written in a different font and saying Installing... I was alarmed and I removed the battery of the phone. Then restarted it and it still had the same screen. I removed the battery again and waited until morning, then it rebooted normally. Home screen randomly creates new pages and moves icons randomly. It is quite uncommon but happened already around 6 times. – gota Sep 23 '15 at 12:51
  • That Android logo part, was it showing "Installing" or "Android is upgrading"? Did it happen after the boot logo or at some other point? As for home screen, did you try using a different launcher app? What are your results? And, is the CM build a nightly or stable? – Firelord Sep 23 '15 at 12:55
  • @Firelord I don't really remember!It happened at 3 AM without me touching the phone. No I didn't try another launcher app. I believe the CM build is stable – gota Sep 23 '15 at 13:00
  • The reordering of icons and added pages could be explained by accidental touches. For example when it is in your pocket. That has happened to me too. You mean the installing part was in your notification drawer? It could just be auto-update settings. Perhaps an app you use changed logo. Significant drop in battery performance and random reboots can happen, your device is already a pretty old model for smartphone standards. It could be a false alarm but it's good to be careful :) – miva2 Sep 23 '15 at 16:49
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Reinstall stock ROM with odin with factory reset and install Avast Antivirus

A tutorial to reinstall stock here

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    There isn't enough considerable evidence that there is a malware installed in the device, so the recommendation of an antivirus, especially Avast without any metric seems to be unwarranted. Also, the site expects self-contained answers so please quote/add the relevant stuff from that link into the answer here. – Firelord Sep 23 '15 at 13:23

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