OK, Project Rubicon and Genesis...What the HELL???
1) So, someone magically managed to create a SINGLE computer chip which somehow is a perfect back door into EVERY nuclear weapon silo in the the entire world, no matter what country they are in, how their systems were designed, and COMPLETELY bypasses any physical failsafes invented, with the capability to shut down a launch, or arm and launch warheads. And every single silo was based upon the EXACT same computer language that ONLY Felicity's dad can hack. Huh. Well, this is a universe that has technology which can shrink people and make people with broken spines walk again, so OK...what the hell, let's say it could be done...
2) Said chip arms and activates EVERY nuclear weapon in the world, and then commences with a TWENTY HOUR COUNTDOWN? I'm reasonably sure that in the real world if we had to launch a retaliatory nuclear strike, we wouldn't have to warm them up for TWENTY HOURS beforehand. Crap...North Korea just launched an ICBM at us? Shoot...we'll get our revenge tomorrow after our nukes warm up. (That's kind of the cornerstone of "mutually assured destruction" and why the world has never caved to nuclear armegeddon, right?) But let's say that Damien Darkh is enough of an idiot to WANT a twenty hour countdown in the typical moronic way that the bad guy monologues his plans to the hero when he thinks victory is at his fingertips...which then leaves him open for #3:
3) Nuclear weapons preparing to launch without authorization, and silos FULL of technicians that are responsible for maintaining, repairing, and in general WORKING on these systems as part of their daily duties. Yet in TWENTY hours' time, NOT ONE of these groups of morons can say "Wait a minute, the big cheese didn't give us an OK to launch a NUCLEAR WARHEAD today, maybe we ought to go out and disarm it? To, y'know...prevent worldwide annihilation?" Of course not. Apparently every country has a military force consisting of nothing but chefs and NO ONE IN A NUCLEAR MISSILE SILO WOULD POSSIBLY BE ABLE TO DISARM THEIR OWN WARHEAD!
I could go into it more (Oh, within a few seconds, we magically stopped EVERY nuclear weapon launch EXCEPT one (so Felicity can blame herself for nuking Podunk, USA and drama drama drama next season as she continues the pity party) and really, someone built an ENTIRE CITY under Starling City and we never noticed? (Thank goodness that doesn't require...oh, a crapton of resources or anything.)
OK, so any superhero movie/show has a certain level you should suspend your disbelief (It's MAGIC! We can shrink a man to the size of an ant! We can resurrect people! It's Time Travel! I gained superpowers from radiation), but don't treat your audience like idiots. I can get there on those kinds of things...but this was some of the worst, laziest, most contrived writing I've ever seen in a series that deserves and has normally done better.
Blah.