Here's what I did the first four weeks on this program.

1a) Parallel-grip chinup, 3 x 6-10, 90 sec. rest
1b) Palm-in dumbbell shoulder press, 3 x 7-9, 4-6, 8-10, 90 sec. rest
2a) Hanging leg raise, 3 x as many as possible, 60 sec. rest
2b) Face pull, 2 x 8-12, 60 sec. rest
3) EZ-bar curl, 3 x 8-10, 90 sec. rest
Jump rope intervals. 60 sec. on/30 sec. off
Sprint or bike intervals
Light jump rope, 15-20 min. 
1) Bench press, work up to a 5RM, then one set at 90%
2a) One-arm dumbbell row, 3 x 7-9, 4-6, 10-15, 60 sec. rest
2b) One-arm incline dumbbell press, 2 x 6-9, 60 sec. rest
3a) Cross-body hammer, 3 x 6-9, 60 sec. rest
3b) Dead-stop triceps extension, 4 x 8-12, 60 sec. rest
Sprint or intervals on the bike
1) Squat, work up to a 5RM, then one set at 90%
2) Deadlift, same as above
3a) Macebell gravedigger, 3 x 10-12, 90 sec. rest
3b) Glute-ham raise, 2 x 6-12, 90 sec. rest
4) Prowler push, 20 x 1
Light walk. 30 min.
The program was designed by MF's own chief training adviser, Jason Ferruggia. I've known Jay for five years, and in that time, he's come to be my most trusted resource, especially when it comes to building muscle and strength. I'm certainly not the only one who views him so highly. Jay is known in the industry as the "strength coach to strength coaches". Many highly popular trainers and coaches around the world perform Jason's workouts in their own training, and seek out his opinion on their theories. (This includes many of the top guys who work for a certain other leading fitness mag). Feel free to check him out on his site. With such a challenge ahead of me, I couldn't see myself putting anyone else in charge of my training.
The goal was to build or at least maintain as much muscle as possible while chiseling off the body fat in only 12 weeks. I knew it was going to require all-out focus and effort, but I couldn't forget that I'm a human being, not a machine. I've come to accept that I have (sadly) very average genetics, and I haven't had much more physical activity than lifting weights and the very occasional cardio session since I graduated from high school P.E. Therefore, I needed a regimen with just enough intensity and down time built in to stimulate the muscles and give them a chance to recover.
That's why I wasn't doing a lot of sets per exercise (and if you listen to Jay, you'll see that's rarely necessary anyway), and my workouts lasted under an hour.
Because I would be sprinting, probably the best and simplest form of cardio for fat loss, I needed to keep all the leg training on one day to ensure recovery. That meant a double dose of squats and deadlifts on the same day. Fortunately, I spent these Saturdays at Jason's gym, The Renegade Gym, in Watchung, NJ. This is where Jay trains many an athlete and plenty of other big brutes to the sweet sounds of Public Enemy and The Rollins Band, so keeping my intensity up wasn't a problem.
Monday's upper-body training was a lighter workout, more to get a pump and encourage recovery, while the Thursday sessions were heavier. Working up to a rep max (RM) was crucial to gaining the strength I wanted. If I could recommend only one method to use to pack on size and strength fast, it would be this one. Just warm up, keep your reps low, and perform several ascending sets until you find the load that lets you handle only five reps. Bang out the set, then back off with 90% of that weight. Since recovery has been such a concern in this program, that's all the heavy work I really needed.
I'd like to add that I put about a quarter-inch on my arms from all the direct arm work in this plan. Part of the reason is that I hadn't done curls or triceps extensions for a year or more (my arms got trained through chinups and presses), so my arms responded well to the change. Still, that's a good gain when you're cutting so many calories from your diet (I will discuss this soon).
You may not be familiar with some of the exercises above. The macebell brings new meaning to the term "getting medieval on your ass". It looks like a giant mace, a big bar with a weighted ball on the end, and I swung it in a shoveling motion. It kind of felt like I was digging a grave (perhaps my own), and the dirt was resisting me the whole time. This fucker worked my abs harder than any situp. Three sets of 10 to 12 was plenty.
The glute-ham raise is a piece of equipment every gym should have. Instead they offer leg curls and butt blasters, and that's a damn shame. The glute-ham works the hamstrings in both their functions--bending the knees and extending the hips. No other machine, and few other exercises, can do that.
The Prowler is a kind of weighted sled that has many uses. My job was to push it the length of Jay's gym, rest a few seconds, and push it back. Over. And over. And over again. I did 20 sprints with it. A great piece of equipment. What's that, you say? "Why not use a treadmill?" "Elliptical machine?" Give this a try. You'll quit doing cardio before you ever go back to a stair stepper again.
I'll save the discussion of my other cardio activities for another day.