I always thought that the burst of static after closing the final terminal was Durandal teleporting you aboard the Boomer. Whether this is after Durandal's trip to Earth and back to throw humanity a few proverbial bones or before (yes, leela said he left, but we know from the later games that Durandal is good at hiding), I don't know, and I don't think it really matters either. Let's look at that terminal:
"
The Pfhor ship vanished about twenty minutes ago, after
venting nearly a thousand Pfhor bodies and other refuse. I am
positive that Durandal is in control, and fear what he might
do with such a powerful ship during the Jealous stage of his
Rampancy.
***END MESSAGE***
"
Nothing about "prepare for teleport", and twenty minutes sounds like a reasonable amount of time for Durandal to fold over to Earth, drop a box of floppies off at Earth, and fold to the other side of Tau Ceti to pick you up, before going off to look for Lh'owon at the galactic core. For a hyperintelligent AI like Durandal, 20 minutes is also plenty of time to re-evaluate a situation and decide "hey, that guy might be useful after all".
As for the discrepancies between M2 and MI, maybe there really WAS a W'rk in Lh'owon's sun, and when the Trih Xeem cracked it, and the W'rk got out. The thing is, we never really get a good image of exactly what the W'rk actually DOES. My theory is that the W'rk is the mechanism behind the fracturing of the timelines you see in MI. Durandal describes it thus:
"Now I fear what that weapon has unleashed will destroy us. I once boasted to be able to count the atoms in a cloud, to understand them all, predict them, and so did I predict you, but this new chaos is entirely terrible, mindless, obeying rules that I don't comprehend."
A timeline-multiplying entity too complex to understand which bends the laws of causality sounds like a perfect fit for this description. (Plus, I love the abject terror you can hear in Durandal as he finally realises that "There's always a bigger fish").
The M2 final screen could be what happens (or would've happened) without the interference of the W'rk, but the timeline is fractured, again and again until one timeline manages to contain the W'rk. I.e. the W'rk only has to be contained in one timeline for its effects to cease and time to return to 'normal', in a sort of "groundhog day" effect.
Another interpretation is that the M2 end screen is NOT a contradiction of the Infinity story. All of the things mentioned in M2's ending screen also happen by the end of Infinity: The Pfhor get trounced by the S'Pht, Leela is still hanging about on Tau Ceti, Tycho is still with the Pfhor, and Blake (as far as I can tell) still gets away after activating Thoth. The only thing different is that Durandal is now Thoth|Durandal, but I don't think the M2 end screen has anything that really proves that "Durandal" is not actually Thoth|Durandal; especially that he/they refused to tell about what they knew about the Jjaro (balance, remember?) and that he didn't want humanity to forget him. Most notably: it never mentions the SO, who was freed to "go" and wouldn't be seen with Durandal.
