Mdthbs

After the system hanged while downloading some video files, then I restarted, I was - and still - able to log in, I found my main UbuntuMate (16.04 LTS) account folders empty, either those on the Desktop or under main system subfolders like Documents, Downloads (except most few recent files that were being downloaded during the system hanging).

All files and folders on my account were deleted, the desktop shows only one folder of them "Natron portable install folder", and the status bar showing that I have the partition capacity free, except 4 GBs.
Later, I found that happened too to the other account on the same UbuntuMate system: all folders there are empty of files, but files on Destop were not deleted.
There are also some NTFS partitions with tens of Gigabytes of encrypted and unencrypted folders were totally emptied.
Some other NTFS partitions on that same HDD were intact.
I looked at that HDD from a live CD, and found that there are two unknown partitions have been created and have empty Linux filesystem folders on them, with each partition of them has almost all the space free too, as if they are just empty hierarchies of Linux installs. Each one if 20 GB, most of it is free.

The filesystem is ext4 for the Linux partition (and the two weird empty Linux install partitions too are ext4), and NTFS for other partitions
Everything in the system is mostly default, as I'm trying to stay aways from proprietary software. I had some opensource tools recently installed though for managing PDFs and code editors. Had many games installed and uninstalled from Synaptic few months ago.

I also had a memory card used to take files for print at a service shop, but not sure if that Memory card carried a virus or not.. I have no anti virus on Linux or Windows.

I have two Windows installs on the other HDD, Windows7 & and Windows XP, which I used recently to prepare Javascript-enabled Adobe Acrobat docs for printing, while the Memory card was attached to the machine. They are dual boot from the Ubuntu loader.

I had also two other memory cards attached to the machine at that time, but none of them affected. All my Memory cards are DOS or NTFS.

So, the machine has:Two HDDs, one for Ubuntu partition and NTFS data partitions, and another HDD for both Windows partitions, and two permanent data memory cards, and a third temporarily used memory card.

Either if this is a hacking attack, or a software/hardware issue.. how would you go around it? What is the easiest and fastest way possible to restore all these deleted/disappeared data?

I am thinking about making clone copy of each of the first HDD data NTFS partitions that survived the deletion using Clonezilla.
Then work directly on both HDDs affected partitions by trying restoring the original partition table, etc., before using Photorec or similar apps to restore everything possible. It will be a real mess of pile of thousands of files! If you know any better workaround, please advise!
Thanks!