I'm making a special installer for an embedded system where I'd like the kernel to boot up, execute a set of things very late in the process where the peripherals have been set up and then reboot the system without the login prompt ever happening.I'm vaguely familiar with init and runlevels, I presume at this point that this is how I'll most easily achieve this. Can I put a script (then where/how?) in the init sequence that runs my stuff and then puts the machine to a reboot afterwards ?If it matters the rootfs is debian. 
Late running of scripts during bootup, ending with a reboot without the login prompt
embedded;init script;init.d
For Debian 7 and earlier, the easiest option is to put your code in /etc/rc.local. This runs at the very end of the boot sequence, just before the login screen is displayed when you boot into console mode, or just before X is started otherwise. Until this script exits, nothing else happens, so if you reboot the system at the end, you may not see a login screen. If you do, it should disappear quickly.I specified the Debian version above because Debian will be moving from SysV init to systemd in the next major version. While it is likely that this future version of Debian will still allow rc.local and such for backwards compatibility, you'd really want to do it a different way for systemd. That's out of scope for this question, though.More broadly, embedded Linuxes don't have to follow the rules established by desktop Linuxes. Dedicated embedded Linux distros allow you to customize things like how the boot sequence works, specifically to cope with issues like the one you're facing.