There is so much to do in Africa it really is going to be dependent on what type of feel you want for your campaign.
Off the top of my head things that the outfit could wind up involved with:
-Desert Wars
- Artifact Hunting/Retrieval
- Poaching/Poacher Hunting
- Supply Raiding
- Extermination
If you're wanting a more light-hearted tour, they could be pulling extractions, or disruptions on the Desert Wars, poaching rare awakened animals in the congos for talismongers, raiding local corporations/merc outifts, etc.
For a darker grittier campaign, they could be hunting down local insurgents trying to destroy pockets of rebellion. As the tour goes on they go from hunting the rebels to burning down their homes and hiding holes effectively going from mercs to death squads. See how the players react to becoming the bad guys. Rather than a betrayal, this may lead to them fighting back against the machine and creating them into shadowrunners.
Last time my players wound up in Africa they were trying to help retrieve an ancient artifact that would help uncover a lost treasure believed to be hidden away deep in the congo by Nazi's during WW2. As the campaign went on, the kept finding themselves one step behind this jackass that was trying to find the same thing. By the end they realized that they were those corporate merc assholes that always seem to be chasing Indiana Jones/Nathan Drake. Then they found the treasure.
It was a sacrificial urn. When a victim bled into it, a powerful Shadow Spirit (I used the stats for Chin You from pg. 123 of Ghost Cartels, a Force 9 free Shadow Spirit) summoned and shredded the victim (read as the sacrificial lamb). The Sprit then gave one service to the nearest mage.
Of course they wound up having a massive fight in the room that resulted in the shadow spirit being summoned and, after a very very bloody battle, killed rendering the artifact just another priceless piece of art.
As for making the Congo feel different than city running, remember some of the key differences. Humidity and Heat are going to make wearing heavy armor a real pain in the ass. Ghost Cartel's set a standard of a "fatigue test every 10 minutes during the day, 20 minutes at night" for wearing non-environmentally adapted armor in the Amazon. I don't think I would go that far, but I'd force it if they wore more than half their encumbrance (effectively making armor encumbrance = Body) or anything obviously dumb (winterized coveralls for example, or Form Fit Body Armor, wrapping yourself in a full body condom is not going to be good in the rainforest).
Likewise, it's a dirty and humid place which is bad for electronics, guns, and general equipment. The rules given for them are: "Each day a non-environmentally adapted fi rearm or electronics device is used, roll 1D6. If the result is a 1, it jams and must be cleaned with a Logic + Armorer or Hardware (4, 1 hour) Extended Test before it will operate again. If the gear is not regularly cleaned, the gamemaster can increase the likelihood of a jam by 1 per day."
Also remember that thermal vision is going to be next to useless in such a humid and hot environment. In addition, the Jungle is going to be teaming with life and noise on the astral plane causing some penalties to assensing tests made there. In the Congo there will likely still be "savage" tribes active that may or may not be hostile.
The rough dirt roads may occasionally have convoys passing by related (or unrelated) to the runners. If the runners are traveling as guards on a convoy, remember that roads wash out, easily in such areas and that a favorite tactics of guerrilla types is to either pit the road and cover with a tarp and sand to wreck the first truck of a convoy (turning around is next to impossible on most of those dirt roads) or to fell trees across the roads to stop them (often felling trees behind the convoy or straight up fragging the last vehicle to keep the train dead).
Help, and reinforcements, are going to be much further away than in the city and getting a hold of new gear, ammunition, cyber, etc. may take a while. Especially if they are out on assignment.
Also keep in mind natural dangers of the Congo as well. Mudslides, man eating plants, snakes (poisonous and constrictors), awakened creatures, shapeshifters, flashfloods, bug spirits, etc. are all possibilities out in the wilderness. Accidental exposure to poisonous animal/plant life or diseases (through bug bites) is also at a much higher potential in the rainforest. Keep in mind if you make your own poisons/diseases, they are a lot less damaging in the SR universe than real life. Try to remember what other deadly toxins deal (such as cyanide) when making them. It may be tempting to be realistic and have mamba venom have a power of 20 or so, but it isn't really in line with everything else. Also keep in mind that antivenoms are (and definitely should be for mercs) available for most venomous wildlife in the areas.
Oh, and if you're forcing them into the Jungle, highly highly highly suggest the Survival skill to them.
