Is this a plot hole? And random stuff...

Is this a plot hole or not?

At the end of the game Alcatraz has gotten inside the alien mothership and got the new signal transmitted that wipes out the alines in NY but shouldn't that same signal go to all the other alien colonies and wipe them out as well?

Also how in the hell did Hargreaves in 1908 managed to work out nanotechnology, and that they would need to make a suit then circle to the present day and we hae the suits that essentially animate a corpse inside. Remember when they did a medical scan of Alcatraz. His heart was damaged and all, much I think he'd be clinically dead, except the suit is keeping his body going somehow.