Much of Axl's story in this game mirrors X's story in X1, such as feeling responsible for the main conflict, fighting former allies as Mavericks, and a mentor giving up their life for them. The main difference is Axl's trigger-happy gusto compared to X's tragic pacifism.
X pulls away from the battlefield despite the resolve he showed at the end of X6, but remember that X salvaged Gate's remains for Alia in the chance she might revive him. Since Gate isn't even mentioned later on, it's a good bet that Alia was denied that chance - viral corruption and Freudian Excuse doesn't change the fact that Gate's actions and skill made him Too Powerful to Live. X may have felt guilty and took up a support position, putting himself physically near her.
Sigma's ultimate goal is apparently to use Axl to get the DNA of X and Zero. This may seem random, considering he's never cared about their DNA until now. But it's possible that seeing what Gate could create with Zero's DNA in X6 (the Nightmare, High Max, and his battle armor) inspired Sigma to give it a shot too. He didn't have any scraps of X or Zero's bodies to use, so he chose to take a different approach and steal it via the fascinating Axl.
Another possibility is that, from the Fridge pages for Mega Man X3 and Mega Man X6, is that Sigma really did suffer permanent damage from Dr. Doppler's anti-virus and the strain involved in flooding Earth with his virus to infect Zero. X and Zero are the only ones with DNA data advanced enough to possibly restore him.
When Red supposedly reappears in the climax, there are several obvious hints that it's actually Axl in disguise. First of all, he gets X and Zero's attentions with a laser shot, an attack that Red has never been shown doing. Then, when he jumps down it makes the same sound as when Axl jumps in-game. The ruse is quickly blown when Red!Axl finishes off Sigma, but it's fun to point out this attention to detail.
It seems kind of weird that Vanishing Gungaroo's stage is in Canada rather than Australia like one would expect, but Canada's similar to Australia in that they're both former British colonies.
In Zero's ending, he has a nightmare in which he and an Ax-Crazy X are fighting to the death. What do you face in the Zero series? An Ax-Crazy doppelgänger of X. Counts as a Shout-Out rather than Foreshadowing because X7 came out after the Zero series began.
Snipe Anteator's pessimistic dialogue with X is another reference to X's original role in Mega Man Zero. Had he not been replaced with Copy X late into the game's development, X would have indeed become a tyrant attempting to build a "utopia" over the graves of rebels.
Vanishing Gungaroo's manchild tendencies are an oddity. Child-like Reploids are not impossible (see Middy and Techno), but they are still level-headed, competent, and mature people. The other outright destructive manchildren are Wire Sponge and Gigabolt Man-O-War, who both suffered from malfunctions. Gungaroo has no malfunctions, so he's just a freak!
