How about this, though, as a second option? Almost directly counters alien missiles, but also reduces the chance that they can be fired in the first place and just improves our destructive capabilities. Reminder that our missiles are currently useless due to the alien plasma shielding.
Design: Earthshatter Missiles (Alien Equipment Token)
The Rockbreaker is an interesting design. An offshoot of our more successful Rockslide missiles, it makes a poor attempt to use alien explosives and whatnot for a more effective missile. It's not great for current use, but it's a good platform to start off of.
The Earthshatter missile is fairly straightforward. It uses a small gravitational drive to move, allowing for extreme agility and speed in the air relative to our older missiles (though it still keeps the aerodynamic shape, as most of its motion will be forward and variations of forward). Taking some tips from alien equipment, we've overhauled the power source employed in Rockbreakers to allow for it to remain fairly stable until detonation, and use it to power the propulsion to save space and weight that would be normally spent on fuel.
A thin alien alloy coating remains in the design from the Rockbreaker, protecting it from countermeasures that would normally destroy a regular missile. However, we've adjusted the coating for a very destructive fragmenting shatter pattern, allowing missiles to inflict damage through both high-speed alien alloy fragments and the Elerium power core blast.
The missile uses a slightly-upgraded version of the Rockslide algorithms, taking some knowledge of what we've learned in it in ventures such as the Brazil computer core. This should just allow for some slightly better targeting from afar, but most importantly, it includes an ability to detect lethal alien missiles and prematurely detonate the missile, using the fragmenting blast to also detonate the alien missile before it reaches allied aircraft.
The Earthshatter should do more damage, be more accurate, be much faster (hopefully allowing in elimination of some alien craft before they fire their missiles), and should increase survivability of our own craft. And it won't blow up prematurely, which is nice.
All of this is accomplished through fairly iterative improvements. Adjusting the coating for fragmenting effect, spending a bit of time re-stabilizing the core to appropriate levels, adding a smaller grav drive (of the same type used in the Talon, roughly), and doing a small upgrade to the electronics based on stuff we've already done with Rockslide computing.
Also.
Here's a revision for later, to deal with infiltration:
Revision: Computer Core Discriminatory Analysis
A revision to the computer core in Brazil, this isn't quite as bad as the name may imply.
Simply put, right now the computer scans for broad patterns on a global scale. It's really useful, but it could be more useful. By giving the computer the capabilities and permissions to temporarily decrease the scope of a scan when deemed necessary, the computer should be able to analyze smaller patterns indicative of suspicious activity that we wouldn't normally recognize.
We hope to use this new feature to locate any aforementioned "suspicious activity" in countries indicative of alien sympathizers or infiltrators. A politician with very strange meetings coinciding with alien visits or alien activity is a more obvious example of what the computer may pick up, and knowledge of this should allow us to pre-emptively deal with alien sympathizers/infiltrators before they strike, and have more intel of alien-compromised entities if we want to act on it further.