1.when I build a dragons den will it help me conqer other colonies easier?2.how do you get crystals&relics3.do you get nukes when you build a dragons den & how do you use a dragon or a nuke on a colony.

1 yes it kills 10% of units and damages the rest to 1 hp where it is used and downgrades ops
2 crystals you get when you reach 20 power and increase resourse production or steal other peoples by conqureing them relics appere and you need to fight to take it and protect it
3 you need build silos or dragons dens then arm them by selecting them and you order them like a normal squad but can be destroyed by ion cannon

What upgrade do i need to build a shield and what upgrade do i need to build a ion cannon

ion cannon lv 5 radar (last one)
shield lv 5 communication center (secondfrom the bottom)

For some reason i cant use my alliance's gate, my squad is on the gate but it still doesn't give me the option to use it.

your squad needs to be at a location with a gate and targeting a location with a gate then under launch it says teleport

What does over head mean

over head is to prevent the strong people to grow insanely strong, so every 100 soldiers you got to pay |0% extra when buying units

Few questions:
A. I got locked down by spy, how long will it last?
B. Spies also damaged my units and units's HP is now apparently 1. Do they regain any HP or will they remain at that low level.

Thanks for answering

In response to your question about your units health, they will regain it all in time. I'm not exactly sure how long you will be locked down, however.