Your mistake is seeing the "Central Servers" as a singular entity for card effects.  The card you are referencing says "ice protecting this server" for the target of effect.

"The Corporation has three central servers: Headquarters, Research and Development, and Archives. Each central server also has a root."  (pg. 6, Netrunner Rules)

If you install him in the root of your HQ server, he affects HQ.  If you install him in the root of a remote server, he affects that server.  "Central Servers" just help define what you get when the game starts, the three components are not protected and affected as one.  Get rid of the idea that there is a single "CS" and a single "RS".  There are three Central Servers when the game begins and you will build 1 or more Remote Servers as you play.  Each Remote Server will house a single Asset or Agenda, have as many root upgrades as you want to affect that single server, and will each have their own defensive line of ICE.

Janus said:

Oh, so R&D. HQ, and Archives each have a Root!

Ok, that really clarifies everything.

thanks.

To Joe K's defense, the whole "Root" concept is quite misleading, as it appears from the diagrams to be encompassing all three central servers. Makes me wonder why they included it honestly.

 Hey, it's never a bad thing to ask.  And yes, the diagram can be interpreted to show a central root for the HQ/R&D/Archives.  And hopefully this discussion will help anyone else that makes a similar interpretation.

On page 9 in the rule book said that Upgrades are the only card type that can be installed in the root of a central server, it did not say that it can be installed in a RS. Correct me if im wrong?

p/s: Its ok, page 13 said otherwise 

There is no contradiction. Page 9 says that, in the root of a central server, you can only install an upgrade (not an asset or agenda). It says nothing about remote servers.

 Just jumping in here (having played the original).

Think of every "Server" as a box, or computer. 

The Corporation starts with 3 "Servers": HQ, R&D, and Archive. These are of a type "Central Server".

The Corporation can spin up any amount of new "Servers" by installing either a) an Agenda, b) an Asset, or c) some ICE to protect it (even if there's nothing there to protect…yet).

These new "Servers" are of a type "Remote Server".

Page #19 confused me initially, until I realized that it shows a single Server (that is a "Remote Server" type) that has an Asset and an Upgrade (both unrezzed). Normally I show my Upgrades Rezzed (and pay the Rez cost) but I suppose you could just "Install" it as a corporation and leave the Running guessing. I mean the Runner would logically KNOW there's an Upgrade there, because no "Remote Server" can have more than a single Agenda or Asset.

If you think of it like computers, imagine each "Server" being a new computer being spun up with software installed (ICE) and hosting a website, or some activity on it (Agenda, or Asset). Or even an office, with a staff of people. You can't have those people working on multiple projects: they're dedicated to a single Agenda or Asset.

Also, you can always install a new Agenda or Asset on an existing "Remote Server" if you trash the existing Agenda or Asset (instead of waiting until the Agenda is scored, or Asset finishes it's life-cycle).

First post, hope this helps!

John Jones 937 said:

… and d) upgrade.

Can u actually start a RS by placing Ice only and then placing an Agenda or Asset at a later time?

 Yes, you can also start a Remote Server by placing an asset, agenda, or upgrade in an empty server and add ice later.

glasswalkerx said:

Think about it this way, all the remote servers are started at the beginning of a game. There are an infinite number of them extending from the play space. They're there, active and ready -- just empty. You can put whatever you want into or on them, in any order you please. Taking things out of them likewise doesn't deactive them.. they're there, just empty.

Mind you, you can only uninstall assets, agendas and upgrades when you're installing something new IN the server, and you can only uninstall ice when installing things ON the server. However, you can not remove ice when installing IN the server, and you can't muddle with the upgrades, agendas or assets when installing new ice ON the server. 

Anarchosyn said:

No, this is off by quite a bit.  A data fort with nothing in it and nothing protecting it does not exist.  If the rules were interpreted as you have given then Bank job would be a much better card, as the runner could simply run on an empty fort.  There are an infinite number of slots available and once something is installed in any of those slots, that fort becomes active.  Also if everything is taken from a Remote Server, that data fort shuts back down. 

As an example, if a corp player plays a pad campaign with no ice protecting it, that data fort is now active and can be run on.  When/if the runner runs on this fort and pays to trash Pad campaign, there is no longer anything in that fort so it becomes inactive.   

Meanwhile, if a Corp player installs a PAD campaign behind a piece of ice and that PAD Campaign is trashed during a successful run, there is still a piece of ice protecting a Data fort, even though there's nothing in the data fort, so the runner can still run on this data fort, even though there's little to gain from a conventional run, but possibly has triggers off of runs that allow for other effects.

Edit: Changed an or to an and to avoid further confusion.

radiskull said:

Technically, you can.   You just have to overwrite the agenda first.  This is often done when a corp has a nice big protected server, and puts an Asset in it to try and bluff the runner.  The runner tries to make a run on the server, and gets all the way through, spending all their money, etc, but then reveals something like an Adonis campaign, which they then dont have enough credits to trash.

On the corps next turn, they can trash the asset and place 'another card' into the server, which again could be either an asset or an agenda.

glasswalkerx said:

Yes!  In fact, it's generally wise to do so.  If you create an RS by just playing an agenda, it will be undefended by any ICE.  If the Runner makes a run against that server, he/she will just immediately access and score it.  Of course, you could try to bluff the runner and make him/her think it's a trap instead of an agenda….or bluff them with a REAL trap.  Ways within ways within ways……>:)