There's no Trojan in the game, you are getting a false positive. When you removed the Trojan, you removed the ability to play the game.
The downloaded version of the game contains Sony's SecuROM, which is actually an uncloaked trojan/rootkit designed to keep you from copying the game (it is completely ineffective in that), but actually is scanning your system for a list of software. If it finds a piece of blacklisted software you will get a meaningless error message.
For instance, Microsoft's Process Explorer software, a simple task manager replacement having nothing whatever to do with piracy, is on the blacklist because its author, Mark Russinovich, Technical Fellow in the Platform and Services Division at Microsoft, was the man who found Sony's infamous XCP (Extended Copy Protection) worm/trojan/rootkit, which was installed on Sony BMG CDs.
When that purposely infected CD was slid into your computer, without your knowledge, Sony installed a very low level (that means ultimately privileged, not primitive) patch into Windows. It masked its presence by forcing Windows not to report the section of the HD where it was installed. Also no Windows program was allowed to show its processes or the amount of resources they used. Therefore the computer's owner had no way of knowing what was installed without his permission. Of course the program which officially did not exist had no way to be uninstalled.
There were three severe consequences to the XCP rootkit. First of all it disabled all of Windows CD copying capabilities. You forever lost the ability to copy any CDs on your system. In addition, since it was cloaked, anti-virus software was unable to scan its section of the HD for malware, so malware was using XCP's cloaking umbrella to hide them too! Finally, parts of the XCP malware were copied from copyrighted products LAME and VLC against their GNU Lesser General Public License.
Mark Russinovich had invented a program called Rootkit Revealer to detect and rat out cloaked malware and accidentally found Sony's little treat. He publicized the thing on his Sysinternals website, causing an avalanche of lawsuits and criminal prosecutions that cost Sony tens of millions of dollars.
Sony was unrepentant, claiming in effect that its right to protect its music overrode your right to control your personal property. They lost of course. But Sony did get its revenge, through its blackmail division, also known as a copy protection scam known as SecuROM.
They included the blacklist, which among other mostly harmless programs, contains the products of Mark Russinovich. When those processes are detected on your machine, Silent Hunter 4 will refuse to run. Ain't it cool to be caught in the crossfire in a pissing match having nothing to do with actually protecting Silent Hunter?
As usual, Sony screwed Ubi, its customer, while doing nothing to protect Silent Hunter 4 against the evil Microsoft Process Explorer. All you have to do is exit Process Explorer, start SH4, alt-tab out, and restart Process Explorer. Then you get:
See the Silent Hunter IV process running, highlighted in gray? The evil Microsoft Process Explorer is aiding pirates all over the world by actually telling its users that SH4 is running on their machine! I'm scandalized! Of course, your eyes also reveal that information, otherwise it would be pointless to run the game.
So there's your trojan. Author: Sony Function: to inconvenience Ubi, which paid tens of thousands of dollars to use this piece of trash. Result: ridiculous ineffectiveness, piracy of your personal property and loss of credibility for a company which effectively demonstrated it has none.