Can't install El Capitan in my MacMini 2009

Just to confirm that you acquired the macOS 10.11 installer directly from Apple using the links provided by @Matti Haveri?

So how far does the install get? I take it that the phase 1 copy process completes, then the Mac reboots. Does the Mac reboot to the internal SSD to go on to phase 2 of the installation where it actually performs more of the installation?

I would remove the Samsung SSD and connect it externally to see if you can get it to boot (it will be slow booting from a USB2 port, but it should be able to boot). This will tell us a lot. If it won't boot externally, then try performing a clean install again on the Samsung SSD while it is connected externally to see if you are successful this time. If this works, then you have some sort of hardware issue (some internal failure, or a compatibility issue). If it does not work, then try installing to some other external drive so we can eliminate an issue with the Samsung SSD.

You have to be careful with what SSD you use with older computers. Older Macs like your 2009 Mini have a SATA II controller. While the current SSDs use a SATA III controller which is supposed to be backwards compatible with the SATA II controller used on a computer.....reality is that some SSDs are not able to auto negotiate the SATA Link Speed. For older computers like a 2009 Mini, your best option for an SSD is the OWC Mercury Electra 3G SSD since this SSD only uses a SATA II controller so there should be no issues negotiating the SATA Link Speed, plus OWC tests their SSDs to make sure they are fully compatible with older Macs.

https://eshop.macsales.com/shop/ssd/owc

I've had success using a Crucial MX500 series SSD in some older Macs....the oldest Mac where I did this was from 2010, but only a few times for a 2010 model (no guarantee since it was only a few Macs & this was for a few users in our organization so I wasn't using them personally). Avoid the Crucial BX500 series SSD as that model is absolutely terrible for several reasons.

Macs can be very picky about the drives they use for booting.

There is a chance the internal drive cable is bad, or the connection is not secure.

You can also try a PRAM Reset to see if it makes any difference (hold the PRAM Reset for at least three chimes).

Is this your workflow:

1. Make a bootable El Capitan USB flash installer and Option-boot to it.

How to download and install macOS - Apple Support

Create a bootable installer for macOS - Apple Support

2. With Disk Utility format the whole internal disk (not just the volumes under it) as Mac OS Extended (Journaled) case-insensitive with GUID partition scheme.

* If you have previously formatted for Ubuntu, you might temporarily 1st have to format as FAT (MBR) and then as in #2 to clear the partition table. Resetting SMC and PRAM might also clear such old stuff.

3. Install El Capitan to the internal disk.

Startup holding the Option (Alt) key and see if you can select the SSD from the Startup Manager.

If not, then there is something wrong with the drive format and/or the install on the SSD.

> Mac still reboots as if no drive was installed

Are you sure the drive is not broken? Or incompatible somehow? Have you tried to install to an external drive?

FWIW I have installed 1 TB Samsung EVO 860 SATA SSD to Mac mini (Late 2009), 2.66 GHz Intel Core 2 Duo and installed El Capitan with that workflow. It works OK and is very fast compared to the old 7200 rpm HDD.