Although they look similar to their weaker brethren, Sectoid Commanders have larger heads covered in thick veins, and glowing red eyes. Like Sectoids, they are all genetically identical clones, but have been engineered with greater endurance and incredible psionic powers. While these gifts make them far more deadly than the lower caste troops they command, they are still ultimately little more than subservient pawns of the Ethereals.
The Sectoid Commander first appears during the tutorial mission in Germany in which it uses Mind Control to force a German soldier to attack the XCOM Assault team. They are not encountered in combat until the assault on the Alien Base. After this point, Sectoid Commanders appear on the bridge of alien UFOs, replacing the Outsider. They may appear individually or in small groups. After the Overseer Crash Site mission is complete, they are replaced by Ethereals.
In Enemy Within they become more common again, as they can now be found in Abduction missions in order to provide Psi Shields to multiple Mechtoids – though this again becomes a possibility only after the Alien Base Assault.
Due to their high Defense and use of cover, Sectoid Commanders can be difficult to hit. Try using Snipers or flanking tactics to compensate for this. If all else fails, explosives such as Alien Grenades and Rockets, which ignore cover and Defense (and in most cases will also destroy their cover to allow more effective follow-up fire), are extremely effective against Sectoid Commanders.
Mind Control is by far their most dangerous ability. If one of your squad gets Mind Controlled, and you are unable to kill the Sectoid Commander within one turn, consider using the Sniper's Disabling Shot or Suppression on their victim to buy yourself more time to kill the alien, which will immediately free your squadmate from its control.
If one wishes to capture and interrogate a Sectoid Commander, the one in the alien base will usually be the most convenient one, as it is alone and will not be too aggressive since it is your first time encountering one.
Sectoid Commander presence on alien ships (whether landed or shot down) is a direct replacement for their Outsider predecessors – thus on larger vessel classes (Abductors and up) they will be encountered in pairs.