The problem originated when I was trying to fix this problem. Things went horribly, horribly wrong and I ended up with a new problem altogether. The last thing I did was run

sudo apt-get install

and that caused my system to freeze. I restarted my computer and it would not boot from the harddrive. I ran a copy of Ubuntu 12.10 from a flashdrive that I had and ran gparted to see if my partitions were all there. It returned this message:

Invalid partition table on /dev/sda -- wrong signature 5208.

The drive appeared as a 2TiB unallocated drive with an error. The drive had 4 partitions before (plus random unallocated space). There was a fat32 partition, an ext4 partition which contained ubuntu 13.04/13.10 (I don't even know which one at this point), an extended partition which contained a swap partition for my ubuntu partition (I was meaning to move that ubuntu partition into the extended partition, never got around to it), and another partition (I don't remember how I formatted it). I should also mention this is a 1TB harddrive.

So in short, I have a corrupted partition table on my primary harddrive from which I boot from, how can I fix this?

I tried mounting the drive with

sudo mount /dev/sda1 /media/ubuntu

then I changed my directory to said folder and tried to list files and this monstrosity happened:

$ ls
ls: cannot access ??w?j^?.: Input/output error
ls: cannot access ??(?
                      ?x?.|: Input/output error
ls: cannot access 6W_@?)?._??: Input/output error
ls: cannot access HB0v???.A}?: Input/output error
ls: cannot access ???.?X: Input/output error
ls: cannot access t)?.+?l: Input/output error
ls: cannot access ?h@   
?.@ : Input/output error
ls: cannot access >?    @??.???: Input/output error
ls: cannot access m???.??: Input/output error
ls: cannot access @ if??a?: Input/output error
ls: cannot access ?M!vN$?.??n: Input/output error
ls: cannot access ?o?
??.Bm`: Input/output error
ls: cannot access ?:I???
M.
: Input/output error
ls: cannot access W??.??: Input/output error
ls: cannot access ?: Input/output error
ls: cannot access ?W?s??: Input/output error
ls: cannot access ?v?k?.???: Input/output error
ls: cannot access 5?$<N??: Input/output error
.x????.??i: Input/output error
ls: cannot access je????.j?1: Input/output error
XjD?.???: Input/output error
ls: cannot access W??n???.?: Input/output error
ls: cannot access ?^x.$"?: Input/output error
ls: cannot access !??*!??j.??: Input/output error
ls: cannot access '-??k?^?.???: Input/output error
ls: cannot access b?w?w?b.\??: Input/output error
ls: cannot access o????"z.??B: Input/output error
ls: cannot access ??b?h.?3-: Input/output error
ls: cannot access ??.$7: Input/output error
ls: cannot access )??K.bk: Input/output error
ls: cannot access s??z?.?(?: Input/output error
ls: cannot access ?F@?0?.@?: Input/output error
.?D: Input/output error
.??: Input/output error
ls: cannot access?????.
                        @: Input/output error
ls: cannot access ?/??
                        ?.??: No such file or directory
ls: cannot access rk?p4q(?.?k: Input/output error

This looks promising. This is the output of fdisk -l

$ sudo fdisk -l /dev/sda
Warning: ignoring extra data in partition table 5
Warning: ignoring extra data in partition table 5
Warning: ignoring extra data in partition table 5
Warning: invalid flag 0x5208 of partition table 5 will be corrected by w(rite)

Disk /dev/sda: 2199.0 GB, 2199023132672 bytes
255 heads, 63 sectors/track, 267349 cylinders, total 4294967056 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x44fdfe06

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1       113305600   894715903   390705152    c  W95 FAT32 (LBA)
/dev/sda2       894715904  1489307647   297295872   83  Linux
/dev/sda3      1489309694  1497307135     3998721    5  Extended
/dev/sda4      1497309184  1953523711   228107264    7  HPFS/NTFS/exFAT
/dev/sda5   ?  3013257822  3688738171   337740175   aa  Unknown