As atlas it depends on the ability you choose, when she uses his smoke bomb (because is low at health) if you choose unestable fissure you can leave a bomb that deals 900dmg in area so you kill her.

Atlas Shield shuts down Skye's Ult completely, so try to read her mind and time it correctly when u believe she has her Ult ready.

Again if she tries to escape his death with smoke bomb if you chose deja vu, you can use setback in area and send her forward away from the smoke, and with less health ready to be killed.