The flight gets diverted to Calgary, where they are met by James Hudson, who has been authorised by Pierre Trudeau to bring Wolverine in. There is a big fight between the X-Men and the newly formed Alpha Flight (Hudson with Northstar, Shaman, Snow-Bird, Sasquatch and Aurora). Wolverine eventually agrees to be taken in, but gives them the slip... so that resolves nothing, really. And so the X-Men finally get back on the plane. Are they really going to make it back to Westchester this time? What will they find there?
This is all a big joke of course. That is: Canadian government acting unethically by running secret unethical operations on human subjects and them forcing them to remain in service is a hilarious concept. Like they would. Over the decades this has been taken so seriously and such a mythology has been built around it, that it's easy to ignore its inherent absurdity and that it's just a short throwaway gag by Wein and Cockrum (embellished, of course, by Claremont and Byrne).