Okay so in a nut shell this is what I was thinking:
1. We could change it so that Smith shoots Dunn in both the chest and the leg and Dunn becomes wheelchair bound.
2. We could have a flashback mission. Not of anything our characters have seen, but what their ancestors have seen. It'll be set in WW2 and the mission is to destroy a Nazi warp hole machine. So we go in, supposedly destroy it, and leave. Little do we know that we didn't destroy it. Then a warp hole opens and Smith comes through. Then later, someone from Boss and Chainer's universe comes through and discovers Earth. He then pinpoints the location of Earth and the leaves, destroying the machine while he's at it. About a month later, Smith comes back to the Nazi laboratory and uses the machines there to make him how he is now.
3. At the very end of the Task Force 589 story, Ace finds out that he's related to Dunn by finding a family tree. By this time Dunn is made a Cpl. and is awarded the Medal of Honor for his sacrifice for the 589. Ace visits him at the "Dunn family reunion" and announces that he is related and shows them the family tree.
4. As for people wanting to make pages not relating to our story, what if we had them make them as subpages of their userpages? Then we could make a non-canon category for them.
If I've forgotten any of my ideas I'll let you guys know.