The sixty second version of the Halo 2 commercial airing right now has three very interesting lines in it. The first is definitely spoken by a Prophet, as we see him speak it. The second, present only in the sixty second version of the spot, may be spoken either by a different Prophet or another character, possibly a Brute. The third, also present in the shorter version, sounds as if it is delivered by the same Prophet as the first line.
"No enemy has ever withstood our might."
On the surface, this is just a bit of Covenant braggodocio. However, it may be possible to draw some conclusions from this about other parts of the story.
For instance, Cortana tells us in Halo 1 that the Covenant fear the Flood. That may be about that specific situation; compared to what we'll see in Halo 2, I think it will probably become apparent that the Covenant units in the first game were undermanned and underpowered.
However, if we take both statements as true and at face value, we must draw the conclusion that either the Flood are unable to withstand the Covenant, or that the Flood are not, technically, an enemy. The latter might indicate a more complex relationship, the nature of which can only now be speculated on. It may not be relevant, depending on whether or not the Flood appear. Very early in Halo 2's development, Bungie were asked about the Flood, and it was said that the Covenant and the Flood have a long relationship.
However, nothing at all has been said about them in the context of Halo 2, nor have they appeared in any movies or screenshots. That they did not appear in any pre-release media for Halo 1 made sense, as they were supposed to have been a surprise. But why keep their inclusion in Halo 2 a secret, if most players expect they'll be back anyway?
The lack of any mention of them up to now either means they are not in the game, or are going to be presented in such a different way that showing them would be a spoiler.
"There are things about Halo even the Hierarchs do not know."
This line is delivered by a different voice than #1 and #2, and is only in the longer version of the commercial. What we know about the Halo is that it was designed to contain and study the Flood, and that it is part of a system of weapons that, when triggered, destroys all the sentient life of sufficient biomass to spread the Flood within the galaxy. This line indicates either other, separate purposes, or perhaps hints at the motives behind those purposes.
Recently I've engaged in discussions with fans who have cast the Flood in the role of a military rival to the Forerunners; a situation that necessitated the construction of the fortress worlds to contain them.
This seems unlikely to me; the Flood, however intelligent, seem to be primarily a parasitic organism with no plans or motivations of their own besides expansion. This might be a military goal, but they don't seem to be using traditional military methods to achieve it. In Halo 1, there is evidence of Human, Forerunner, and Covenant societies: language, literature, technology. There's no evidence of such for the Flood, so the idea of them intentionally developing a military organization for the purpose of conquering and holding territory seems unlikely.
What seems more likely is that the Forerunner, having withdrawn to an area outside the galaxy, and recognizing the Flood as a threat to life everywhere, built the fortress worlds to, at least in part, study the Flood to gain knownledge useful in countering them or beings like them, much as humans keep dangerous infectious diseases for study, and created the system of superweapons as a safeguard against an outbreak; by destroying an entire galaxy's life forms that could spread the Flood, they safeguard other galaxies. So obviously the Flood either have, or could have or obtain from somewhere, means to travel outside the galaxy. That the Forerunners did not simply design Halo to be triggered automatically at regular intervals, thus preventing sentient life from ever developing and thereby giving the Flood a vector to spread, indicates to me that they do have some respect for life, but that whatever they are protecting is more valuable to them then all the sentient life in this galaxy.
"There are those who said this day would never come. What are they to say now?"
This line sounds very much as if it is delivered by the same Prophet who says the first line. It's fairly vague, but it sounds as if some event foretold in a prophecy that was doubted by some-- perhaps by other Prophets, or other Covenant races-- he believes is now taking place or about to take place. That it seems this event involves Earth means that the prophecy in question may be related to the initial Covenant transmission mentioned in Fall of Reach: "Your destruction is the will of the Gods, and we are their instrument." (This line also appeared in the E3 2000 video, delivered by an Elite, speaking English.)
Why do the Gods want humanity destroyed? We'll most likely find out in Halo 2, but ILB might hold some clues...