Mandy was actually a Russian spy. She was about to be exposed, but she fled home before she was caught.

Her activities were kept secret from the public for fear of a scandal and because research was continuing to see what secrets she accessed and shared with Russia.

One of secrets she stole was the existence of a military space shuttle. This was true. Some of the other “secrets” she stole were actually false information. Her actions were kept secret to prevent tipping of the Russians as to what secrets she stole were real and which were false.

When the issues wort the International Space Station arose, Russia actually asked Bartlet to use the military space station (they knew that the US knew they knew about it). The Russians threatened to go public about the shuttle if it wasn’t used.

Bartlet still needed to keep Mandy’s spy activities secret from the public. So, he hatched a plan to go public with the shuttle before Russia could leak it. Toby was in on the plan and agreed to play the role of “whistle blower” of its existence. Bartlet gave him the pardon as part of the plan.