It appears that the Pentagon will retain control over flight codes and key software that controls the F-35 Joint Strike Fighter that Canada is in the process of purchasing.
In theory, this would make it possible for outside forces in the US military to navigate Canada’s F-35s, stop them from flying, control their targeting systems and probably many other functions.
Thus, a large portion of our sovereignty over these jets would be compromised. Canada would not be able to count on its ability to use these jets in any situation disapproved of by the US. Canada would be unable to participate in any multilateral strike force in which the US disapproved.
In the Falklands War, the US considered alllying itself with the Argentinian junta. Though it is inconceivable that it would have gone to war with the UK it is very possible that it might have interfered with the UK force tasked with liberating the Falklands. If this situation was happening in the present, and Canada was helping our ally the UK, it is possible that both countries would lose their ability to use their own Joint Strike Fighters.
While it is difficult at present to conjure a situation in which Canada would be defying US policy in its use of jet fighters, over the long lifespan of these jets there may be situations that we cannot even imagine now.
Given the current turmoil in the US government, it isn’t completely possible to predict US behaviour in the future, and we have only to remember the recent US war on Iraq to realise that there are many parties in the US government that can operate almost independently of the US government and are difficult to manage coherently. Our ability to manage our own sovereignty may rely on the machinations of the increasingly irrational American political machinery.
Perhaps the only thing worse than having overpriced weapons you don’t need is having them actually under the control of someone else.