[farothel]

Always check your player's backstories.  If one comes from the Barrens, have people he knows go missing (maybe his brother, or his father).  That should at least keep him interested and he can then drag the others along if they start to wander off.  Some positive and negative qualites can also be used for this purpose (lost loved one is the obvious example, but even day job can do the trick if the player's day job is for that company) and the same goes of course for contacts.  If you use those backgrounds then the players will feel like their characters have much more to loose or to gain than just a paycheck.

[DigitalZombie]

Another take on the chip-soldiers would be the knowledge/active skill hardwires from Chrome flesh. They are a lot cheaper and can only take a single permanent skill. For instance Knowledge: small unit tactics 6 and Automatics 6 only costs around 36K all in all. (I suppose you dont need to buy the skill software separately?) And would be even cheaper as Omega or used.

Another idea comes to mind: have the characters unknowingly work and help "design" the skillsofts/personafixes for the badguys

You have the hardware: Check
you have the "soldiers": in progress as more and more gets abducted
You have the knowledge, activesofts and personafixes: not quite- enter unwitting runners

Evil corporation approaches the runner team with some easy money- the runners have to do (insert job already posted here) with a SIM-module and hand over the full recordings of the complete run afterwards. Naturally the corporation will focus their effort on those runners with very high dicepools, believing those to be most appropriate to their new software. And they will naturally try to urge the characters into being aggressive and shoot first, questing later.

Evil corporation will then use the streetsams combat experience as a base for their own chipped soldiers. (with some added quirks from the streetsam- maybe the chip-soldiers starts talking with the characters accent, or manifests some of their mental/social flaws or weapon preferences etc).

Naturally when creating the persona fixes the corporation would erase all unwanted characteristics like an unhealthy hate towards the established corporate world and a preference for a more anarchistic lifestyle. But because of working under a budget they would most likely overlook stuff like addictions, biased and such.

Suddenly the characters are up against cheap copies of themselves

[adzling]

according to Wak (the freelancer responsible) you do need to buy the software....

Another take on the chip-soldiers would be the knowledge/active skill hardwires from Chrome flesh. They are a lot cheaper and can only take a single permanent skill. For instance Knowledge: small unit tactics 6 and Automatics 6 only costs around 36K all in all. (I suppose you dont need to buy the skill software separately?)

[Talgrath]

My thought, as far as the soldiers, would to be to have the "soldierwire" system make the soldiers similar to the ones from the FEAR video game.  They'll respond as expected when spoken to, more or less, but their minds are basically empty and directly controlled and networked together to make for "perfect" squad awareness and tactics.  If desired, controllers can "jump in" to them similar to a drone by using a unique RC setup.  What would make this system unique is that they're cybered up heavily enough to drop their essence to 0, "killing" them, but they're still able to move about thanks to some sort of mix of cybertech and magic.  As far as where to start, as others mentioned, a great idea is to either have someone from one of the PC's past get kidnapped, or maybe one of their contacts or simply get hired when the corp snatched up the "wrong" person.

[Shadowjack]

Here is how I would set it up.

1. The person behind this project does not have the full suport of the megacorp. His idea was met with scrutiny but he was given the okay. He has considerable power but there are many that don't back his plan.
2. Because his resources are limited and he does not wish to have his reputation destroyed, he has decided to execute the plan under the guise of an organization that helps promising youth from the barrens.
3. Volunteers are brought in by a mix of hope and false promises. They are told that they will be gifted cutting edge bioware but instead are implanted with the new wires.
4. Mr. Johnson has a niece that went missing a few weeks ago and has brought the team together to find her and bring her back. He is unaware of how deep the plot is.
5. His niece was intended to be the leader of the entire army of super soldiers and has not yet been corrupted, although She is held captive by the man behind the curtain.

The ultimate goal is to reach an exciting final session in which the entire organization is destroyed and the man in charge is imprisoned. To make this happen the PC's will need to be highly motivated financially but also from a personal standpoint. You want to work backwards and identify the key parts of the story that need to happen, or at least that you hope will happen.

1. Early sessions are about following leads on the girls whereabouts and finally making contact. She manages to give them a few critical pieces of information, thus exposing the plan of the organization but She does not know who is behind it, only the woman that runs the operation on his behalf. Before the team can rescue the girl, the woman managing the organization shows up and foils the plan with brute force. At this juncture you want to do something that makes the players very angry at this npc. Make it personal and make them feel it in a major way. The main goals are to build tension, establish your villain and have the villain succeed.

2. With the newfound information the team reports to Mr. Johnson and the plot escalates. The team finds clues about the organization but does not have enough information to complete the rescue, instead, they are pitted against the secondary villain we have just established. After some time they encounter said villain and defeat her. After her defeat the team acquires information about the main hideout where the true mastermind pulls the strings. The main villain is aware of this and makes it personal by sending a file to the team through one of his minions. The file demonstrates the niece being corrupted by the wire and the team is threatened with the idea that they will receive the same treatment should not they not withdraw. The villain also has incriminating evidence against the team.

3. The climax will be finding the location of the villain and taking him down or capturing him, both of which will terminate the project, which was not fully supported by the megacorp to begin with. Even though they failed to save the girl Mr. Johnson will have his revenge and the team will feel good about what they did.

Good luck.

[Faust]

A possible setup for this is to have your runners go to the barrens to extract someone from a gang, drug den etc. (simple run) Then find out they have been taken by the corp. since they don't get paid until they complete their run..Legwork leads to plot line.
To get runners to care always mess with their money, Karma and rep. (sometimes family)

[iduno]

You can also have them hired to do some of the kidnapping. It would give the runners a reason to recognize one of the soldiers other than it being a contact/family/friend/etc.

Better if the players have a grudge against a particular corp. That just happens to be the same one Catco is gunning for, giving the runners a reason to help before they find out what their "allies" are up to. Of course it would be best if loose lips (or overheard comlink traffic if the decker is doing his/her job) point to the runners being the next "volunteers" if they are having second thoughts about helping.

I want this to be a big, overarching story, so, taking your advice into account, I'm thinking 7 or 8 runs.  Possibly an additional few side runs, that only tangentially tie into the main plot.

The question then is will your players go for that?  Make a plot too big, and players will forget why they're even on it by about the sixth or seventh session, even if you keep good records on Obsidian Portal or something.  Being generous, maybe half your players will like that, and the rest won't care. 

Perhaps, over the course of 2-3 sessions, they find out about the experiments and put a stop to them, only to learn they stopped this from occurring in one city out of many. That would allow you to try out the plot for a short time, and bail if nobody is digging it. If they are, you can let them find out there is a larger conspiracy they have just stumbled on. After all, it should always be the players' decision to follow the plot thread you want them to.