"Not sure if I am an evil genius, or just someone who watches too much TV"
I am a Texas college student (studying Management of Information Systems), and I am a Tech enthusiast, computer geek and sci-fi fan.
I queue most posts but will do a post dump about once every few weeks.
and since this seems to be the main question you guys ask I am 5'6" tall, so ask me other things (funner things) also before you ask I am taken.
first off I think ten found a way to store the timelord part of Donna (well all of the Donna he knew). most likely using the chameleon arch as it would be an easy way to try to remove the timelord part of her so that she wouldn’t be hunted for it. and from that he uploaded her to CAL.
She would help take care of the kids (as they were hers) and keep River company and such. this fits in a larger head canon that the Doctor is turning CAL into a new Matrix to keep companions safe (and so that he can visit them at night).
Also I think that the doctor set up some more protection for her (more than the regeneration bomb). first off he got some of his friends to help out. Jack for one would help, he could use Torchwood’s resources to keep track of her. Sarah Jane would also help, by befriending Donna and Donna’s Mum, and just making sure that nothing is surfacing with Donna. Martha, Micky, and UNIT would also help.
I have a bit of a head canon that UNIT keeps track of people who have had alien contact and monitors and helps them. Sometimes it’s recruiting them like Martha, sometimes its protection, sometimes its just helping them get set up and leaving them alone, and sometimes it is providing medical care (as some of the medical history and parts of biology (weather its alien physiology, unexplainable damage, or non-terrestrial medical care) might raise some questions in the mainstream medical system).
but back to Donna. the groups would probably pose as Wilfs friends, maybe and astronomy club or something. and Wilf probably wouldn’t mind, he could have friends who he could tell about his experiences and swap stories with (and not think that he is crazy).
also the reason Donna gets this much protection is simple. she is more vulnerable. She can’t remember her times with the Doctor so she isn’t going to suspect that she would be a target. She also wouldn’t remember the stuff she had learned, weather how to BS her self to safety or how to take down a Sontaran.
finally she is a more interesting target, she is a tiny bit timelord (from the meta crisis) and since some groups are VERY interested in procuring timelord DNA (as River said, they would rip the world apart just for one cell). so if she was discovered they would take her and try to extract what they can.
Rose Tyler: The defender of the Earth.
Harriet Jones: The bravest woman in the world.
Captain Jack Harkness: The man that started change.
Sarah Jane Smith: The woman who reminded the Doctor of who he was.
Martha Jones: The woman who saved the world.
Donna Noble: The most important woman in all of creation.
Amy Pond: The girl who waited.
Rory Williams: The Last Centurion.
River Song: The woman who gave the rest of her lives to save her love.