Oh noes, you can't lose to Ghetsis!! If Hilbert/Hilda lost against Ghetsis, then I believe that he would terrorize over the Unova region and wreak havoc on all of the trainers and citizens who have Pokemon. People with Pokemon would have to hide with their Pokemon, but sadly most of the Unova region would lose their Pokemon and Team Plasma would prevail. The Pokemon spunk of the Unova region would spiral down and new trainers wouldn't come to the region because of their fear. The gym leaders would be out of business because they wouldn't have trainers to battle with. The leaders and the elite four would go into hiding from Team Plasma. The Unova reason would suffer economically because most of the businesses deal in some way, shape, or form with Pokemon and they would be out of business. A strong black market would form to sell products and goods to the people that still owned Pokemon. The region would probably also suffer geographically because many places would be overcrowded with Pokemon since most of them would be reverted back to the wild. Also, there would be a sense f gloom in the air which would make the Unova region all sad and depressed. Eventually, if no one stopped Team Plasma most people would move out of the Unova region, but it would do no good because by that point Team Plasma would be big enough to emigrate to other regions and to take those over as well. Other evil companies would hop o nthe band wagon and the evil corporations would have their way with the people in the Pokemon world as well.
Team Plasma would gain their power by after Ghetsis has defeated you, N would cleverly unleash a smoke bomb. Hilbert/Hilda would escape, with all of their Pokemon and you both would hurriedly find a Nurse Joy to heal Pokemon. You would warn people about Team Plasma but no one would believe you. After your defeat, their is no one to stop Ghetsis so he goes and catches Landorus, Thundurus. After that, he catches Terrakion, Virizion and Koballion. He uses these five, along with many other strong Pokemon to defeat powerful trainers and to "liberate" their Pokemon. Eventually, Ghetsis defeats Alder and "liberates" his Pokemon from him. This makes Ghetsis famous and every bad guy or guy that wants power comes knocking on his door to join Team Plasma. Team Plasma gains hegemony and soon the entire Unova region fars them. Team Plasma would then station their mebers in every town of the Unova region. they would search every nook and cranny of the region and would separate Pokemon from all of their trainers. Many trainers would go into heading. The Unova region would be in desolation.
After Hilbert/Hilda and N escape, they are not sure what to do. They train in secret, a place where N only knows, to try and defeat Ghetsis. They hear about Ghetsis' uprising and Team Plasma's new, stronger power. They hear about Alder's loss. One day N dissapears, and Hilbert/Hilda has no idea what to do. Eventually, N comes back with Alder. You start a resistance and Alder becomes the leader. The resistance contains the gym leaders and the elite four. There are also many strong trainers that join the resistance as well. You all meet in private, but some of the gym leaders and trainers wander around the region to see what's going on and to spy on Team Plasma. You eventually build up enough strenth and challenge Team Plasma and Ghetsis again. You defeat Ghetsis and he flees; peace is restored to the nova region! It takes a long time, but things go back to normal and most trainer are reunited with their pokemon. Alder finds his pokemon and you challenge him for champion. You win and are crowned the new champion of Unova region. N scatters off, and becomes a mystery.
If Hilbert/Hilda lost to N, and Ghetsis' real motive wasn't revealed then he would have more success and Team Plasma would be in power for longer and would be even stronger. Eventually though, I believe that a resistance would form and N would turn from hs ways. You would eventually be able to defeat a stronger and more powerful Team Plasma but you would have to have help from gym leaders and elite four members of other regions. More trainers would e in desolation. N would turn from his ways and would live in the mountains far away to contemplate and think of the things that he had done. He would be a sad and gloomy person for the rest of his life; he would be very morose and this would age him. His hair would turn gray quickly. Ghetsis would flee, and try to bring Team Plasma back up. It would be harder to defeat Team Plasma in the future because N wouldn't be as willing to help. Eventually though, N would help and would die helping you defeat Team Plasma in the future.
As for Nurse Joy and Office Jenny. When Unova took over the region they would scatter to other regions where there sisters were. Some would stay and secretly spy on Team Plasma. They would have communicators to spread news throughout the regions. They would form worldwide a resistance to take down Team Plasma as well.