How can I counter Plasma Missiles?
In the base Eclipse game, there is no hard counter to Plasma Missiles. However, there are tactics that work well against Plasma Missile-focused ships.


Cutting off the retreat of missile fleets can be devastating, since they often work best by unleashing their missiles to deal crippling damage and then retreating to fire again the next round. A missile-only fleet with its retreat cut off will be annihilated by even a single surviving ship with a single cannon. (And sending another ship with beam weapons to reduce this threat also reduces the potency of the missile fleet, which is what you want.)
Speaking of surviving missile fleets, Improved Hulls are a good way to build a fleet to do so, combined with enough Shields to neutralize the opponent's Computers. Diplomacy will be important because this fleet will be vulnerable to a more traditional fleet.
Many missile fleets will be Interceptor-based, since those small ships allow you to deploy more raw missiles for cheaper. You can take advantage of this by using the large number of Move actions this fleet will require to outmaneuver the interceptor fleet. If the missiles are scary enough, nobody will mind if you slip a cruiser past and neutron bomb that faction's planets.


Should you have a chance to play with the Rise of the Ancients expansion, it contains two rare technologies that act as hard counters to Plasma Missiles: the Distortion Field, which grants a -2 to all missiles that attack your ships, and Point Defense, which gives your cannons a free attack to shoot down incoming missiles. Neither of these technologies requires a component--all your ships get them for free. Rise of the Ancients also features another soft counter in the form of Flux Missiles, which are 1-power missiles that also provide an initiative bonus. These are powerful against the traditional fragile Plasma Missile fleets.