The first thing to notice, as you enter a level named Prison Sex, is that Tempus Irae 2: The Lost Levels is definitely not for the younger set, as it contains explicit lyrics, some rather horrific images and text, and the world's only X-rated map view. So, all kids out of the pool... for adult swim :P
With that out of the way, TI2's levels are much larger and more difficult than those of the original TI. This is clearly noted in the readme, but it's worth comparing it to Marathon Infinity in that respect. Once the restriction of keeping the scenario doable for less-skilled players is lifted (not to imply there's anything wrong with said players), the mapmaker can create situations with much higher "minimum requirements" on all difficulty levels - Major and Minor monsters aren't all that different when they're hitting you from three sides and you have only 3 shotgun shells and a half-full AR to defend yourself with. I'm still playing on Normal, of course, but it's still a big jump between the scenarios.
Several things about this level strike you as you start out. First, the monsters are significantly stronger than the typical population of a TI level. Major Hunters and Troopers greatly outnumber minors, MOAHs abound, all Drones are major (like that makes them any more dangerous :P), all Cyborgs are the "gold" variant that was present in Infinity but not used (and they all have guided grenades), the Enforcers are the yellow variant previously seen only in secret levels, and the Fighters are all the "champion" fighters from You Think You're Big Time (and Game of Death). They are tremendous ammo sinks, taking an entire clip or more from the rapid-fire weapons or several shotgun shells to kill; the rocket launcher or the flamethrower you find later in the level is the best weapon to use on them.
Secondly, the map is very large and complex, equal to the largest of TI's. The map has over a thousand polygons in it, spread out over several overlapping levels, making the map view less and less useful as more is revealed; this problem affects virtually all very large Marathon maps, including several in Marathon Infinity so I'm not going to "deduct points" for it, but it's an extra irritation when backtracking. You will be doing some of this in the level too, and without a clear destination, and given the huge size of the level and the fact that according to the spoiler guide some areas were deliberately designed to slow down the player it's quite irritating.
Thirdly, TI2's plot is not nearly as coherent as TI's was. In fact, I'd say TI2 doesn't really have a plot, just a set of related terminals on each level. There are least 3 points in the scenario where the setting and story simply change, with no explanation or reason. It feels like exactly what it is: A plot thought up after the fact to tie all these pre-existing levels together. This makes TI2 less of a "story" scenario than a showroom of advanced mapmaking, which is something it does very well but don't expect any complex layers of narrative to unravel (at least for a while). On this level, you're in the middle of dealing with some sort of prison riot when a S'pht entity breaks through and requests your services. The "prison" storyline isn't going to be continued, and the next level is a clean break from this one in every way (as Marathon development progressed, the number of Rebellion levels per scenario seemed to increase...)
There's one major secret on this level- in a corridor with a brown stripe running along its walls, tab the center of a T-junction for an Enforcer and an invincibility powerup.
