Excellent, excellent. I have a couple ideas to add.
One element that I believe would really enhance the gameplay would be creating the appearance that the user has actually made a minor change to the timeline. The easiest way to do this would be to have a few fake websites for fictional organizations ready to go online at the drop of a hat. Once some task has been completed, ta-dah, it exists. The next missions the user would receive would then involve either investigating the new organization(s), or changing the timeline back to a state that doesn't host the new powers. Once they undo their timeline blunder, ta-dah again, they get a 404 error every time they try to go to the website after that. Obviously, this plan would only work for teams of users working together in the game. It wouldn't be worth it to create and take down a website repeatedly for every individual user that played.
Another good immersion tactic is to frequently allude to MAJOR timeline blunders that happened in the past but are now fixed. Such alternate timelines can have rich, detailed histories that never happened. We can have a few of these in "chronopolis records" for the dual purpose of warning agents of the gravity of the work they do, and for studying cause and effect. The best part about this technique is that alternate histories of the earth are already all over the Internet and the majority of the population isn't familiar with them. We can just say that those real people who are familiar with the histories are actually time travellers themselves, either fellow agents, rogue agents, or enemy agents. If someone gets offended about borrowing their story for our game, we can just apologize and remove all references to their material, and call THAT a timeline change, or perhaps just blame the deletion on internal Chronopolis politics. Here is a good sample alternate earth history:
http://www.nada.kth.se/~asa/Game/Fukuyama/bigd.html
