R.U.S.E. takes place during World War II. The game contains a single story arc, portrayed through the perspective of Joseph Sheridan of the United States Army. Sheridan, a Harvard dropout, joins the U.S Army and eventually assumes control of the First Armored Division. The game opens in 1945 as General Sheridan liberates Colditz Castle to free an undercover operative, code named Nightingale, who knows the identity of an Axis informer, code named Prometheus. Sheridan then reminisces to 1943 when he was a Major during the Allied North African campaign when leaked information led to devastating Allied losses at the Battle of Kasserine. Sheridan meets British intelligence officer Colonel Andrew Campbell, and working together, in spite of Sheridan's inept commanding officer General Weatherby, they are able to turn the tide of battle. Sheridan is promoted to Lieutenant Colonel for his efforts.

In 1943, Sheridan takes part in the Battle of Monte Cassino, and while he disobeys Weatherby's direct orders to confuse German intelligence, Sheridan is able to push the Germans back and open up the road to Rome. Sheridan is promoted to General and meets Kate Garner, an attaché from the American War Office. At a victory party, Campbell remarks that the Germans are not fully defeated yet and that Sheridan is turning into Weatherby now that he has been promoted.

In 1944, Sheridan is in command of US troops landing at Utah beach on D-Day, with Weatherby in command of Omaha beach. Sheridan is able to secure a beach head and defend it against counter-attacks despite Weatherby's inability to secure Sheridan's flank. The operation in Normandy is hampered by inaccurate information given to Campbell by the French resistance; this, along with remarks from Kate, strains Sheridan and Campbell's friendship.

Later that year, Sheridan is placed in command of forces in Operation Market Garden, and Weatherby is discreetly placed in command of forces "in reserve". After an exchange between Campbell and Kate, Campbell remarks that he cannot offer the same "incentives" as Kate and states that he will request a transfer. Despite Kate's insistence that Joe has "outgrown" Campbell, Joe is still clearly bothered by the British Officer's departure.

Despite deeply inaccurate information on Axis forces in the area, Sheridan is able to keep "The Highway to Hell" open. However the British forces at the final bridge to be secured are forced to surrender, thus ending Market Garden as a failure. Kate leaves for Washington D.C. for a new "promotion" leaving Joe feeling sorry for himself.

Three months later Sheridan and Campbell meet on the Belgian front, and the two make amends, with Sheridan apologizing and telling Campbell that "he was right and that they should have listened to Campbell". With Campbell's help Sheridan manages to hold onto the key city of Bastogne during the Battle of the Bulge. During the siege, General von Richtor, a German general who gave Sheridan much trouble in the past, personally requests Sheridan surrender. He reveals that the Germans have received orders not to take prisoners of war any more, but despite this, offers to guarantee the safety of Sheridan and his men if they surrender honorably. Sheridan refuses, only demanding to know how an honorable man like von Richtor could serve the Axis. After pushing back the German offensive Sheridan and Campbell interrogate General Von Richter upon capturing him. Learning that only the head of the German Intelligence Service, the Abwehr, Admiral Canaris, knew the identity of the spy Prometheus, but the Admiral had been arrested for plotting to kill Hitler.

Returning to the present, Sheridan, Campbell and the undercover agent, Angie, head for Torgau on the Elbe to supposedly meet up with the Soviets. However, the meeting turns into a race to reach the secret weapons research facility in Torgau before the Russians do. In order to avoid a "diplomatic incident", Sheridan receives help from an unlikely ally: General Von Richtor, who also does not want the weapons to end up in Soviet hands. Under the cover of Von Richtor's German troops, Sheridan and his men reach the weapons facility in the Soviet zone and destroy it. In the process Sheridan learns Prometheus's is his former attaché Kate Garner. It is revealed that Kate had not only been giving intel to the Germans on the American forces but that she also had been giving intel to the Soviets on German weapon research. The weapons in question are long range V2 Rockets equipped with nuclear warheads. Despite having destroyed the research facility Sheridan learns that Kate had already moved several rockets to another location.

Sheridan and Campbell prepare to attack Kate's base and destroy the weapons, but are forced to re-think their strategy when Joe receives a warning from Kate that she will use the V2 rockets if they continue to provoke her. Sheridans assures Kate that he won't back off, and Kate simply responds that Sheridan will be "rolled over by the modern world" as communism will be inevitably victorious. Good news arrives when the Soviet Government declares the 8th Guards Army (the branch of the Soviet military Kate was working with) is an extremist renegade faction and Allied Commander General Eisenhower orders a full scale assault on Kate's base. With the help of some newly developed nuclear equipped artillery, Sheridan manages to destroy Kate's base, destroying the German nuclear warheads and killing Kate in an atomic blast. At the end, Sheridan expresses his wish to take a vacation and see Europe "without the bullets".