Missile Silo Tutorial
Properly used, the Missile Silo can be detrimental to even the most extreme fortifications. It is not cheap, so it should be used when only conventional weaponry fails.
Missiles are built directly by the silo. While any number of them can be queued, construction will halt when all four spots are occupied.
All missiles in the silo can be launched at the same time by having the silo selected. To fire a single missile, select it individually and use the regular attack command. The Force Fire command can be used to hit an arbitrary location within its range. A missile will not fire at a target that is out its range regardless of the command given.
Damage can be dealt to single structures or over large areas. The Eos does 3500 damage within a small blast radius. Aim for spots where multiple buildings touch to apply this damage to more than one building. If there are bigger clusters of structures, the Inferno can be used. It has a much bigger area of effect.
Shields and Terraform
Every missile except the Shockley will be stopped by full shields. If the shields are slightly below full charge, the Eos can pass through them as well. Shields can be circumvented by either stunning or weakening them before firing the remaining missiles. For a successful stun, first scout all Aegises and then use Shockleys to stun them. The Shockley has a small AOE. Multiple stuns might be needed to deactivate all shields if they are spread out. Alternatively, an Eos can be used to weaken all shields in a shield network. After firing one Eos, any following Eos will pass freely through the shields if the shields get a few seconds to equalize their charge.
Terraform can be flattened by the use of a Quake missile. Those have a high trajectory, so you have to target them at the terraform. They don't pass through shields, even at low charge. Alternatively, the AOE of the Eos or Inferno can be used to do damage through terrain.
Timing and Trajectories
The trajectory of the Shockley and Quake missiles is much higher than that of the Inferno and Eos. This results in longer flight time and allows them to mostly ignore terrain.
Account for the additional flight time of those missiles. Firing them at the same time as low-trajectory ones will result in Inferno or Eos reaching the target before the defenses are stunned or the terrain is smoothed.
Firing multiple missiles in quick succession is often preferable to firing them simultaneously. When the enemy has multiple shields, a small delay between missiles ensures that the damage is spread over all shields. This way, the other shields can't block the remaining missiles as they would if the missiles were fired simultaneously.
Fire one Eos, wait 2 seconds, fire other 2 Eoses.
Terraformed Shielded Advanced Geothermal
Either fire a Shockley at the shields, wait for it to impact, and then finish it off with a Quake followed by an Eos, or try to splash-damage it by aiming 2 Eoses at either the back of the moho or the base of the terraform.
Fire 2 Shockleys to stun it, finish off with Raiders. Re-stun with a single Shockley after 40 seconds if needed. The same works for Detriment with 4 Shockleys.