Originally posted by Silent Master
They did it from inside so that they could deliver the nuke and destroy the mothership. it was already shown the alien shields wouldn't stop the signal when they used it to shut off the shield in Area 51.
True but iirc they had to infect the mother ship in order to affect all the others. Or else they would have to infect each ship one at a time. But I certainly could be wrong as I have not seen the film in years
Tony takes out the shields wirelessly. He hacked into secret government servers using his (assumed designed by himself) cell phone in a matter of seconds in IM2.
Alien tech that could be hacked by a guy with far fewer tech feats than Tony with a 90's Mac will pose little to no problem for current day Tony and F.R.I.D.A.Y.