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Continuing the story from his Wiki page:

In March 2011, Aleynikov appealed the conviction, asking the Second Circuit to review the District Court's decision denying his original motion to dismiss the indictment for failure to state a claim.[9]

On February 16, 2012, the United States Court of Appeals for the Second Circuit heard oral argument on his appeal and, later that same day, unanimously ordered his conviction reversed and a judgment of acquittal entered, with opinion to follow.[10] Aleynikov was released from custody the next day.

On April 11, 2012, Dennis Jacobs, Chief Judge of the United States Court of Appeals, published a unanimous decision in a written opinion[10] stating:

On appeal, Aleynikov argues, inter alia, that his conduct did not constitute an offense under either statute. He argues that: [1] the source code was not a "stolen" "good" within the meaning of the NSPA, and [2] the source code was not “related to or included in a product that is produced for or placed in interstate or foreign commerce” within the meaning of the EEA. We agree, and reverse the judgment of the district court.[9]

In the course of these events, Aleynikov has spent 11 months in prison. Aleynikov has divorced, lost his savings, and his career is ruined.[11]

The government did not seek reconsideration of the Second Circuit's ruling, thus ending federal action against Aleynikov.[12]

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Although the Court had long accepted in dictum the principle that prosecution by two governments of the same defendant for the same conduct would not constitute double jeopardy, it was not until United States v. Lanza[53] that the conviction in federal court of a person previously convicted in a state court for performing the same acts was sustained. “We have here two sovereignties, deriving power from different sources, capable of dealing with the same subject-matter within the same territory. . . . Each government in determining what shall be an offense against its peace and dignity is exercising its own sovereignty, not that of the other.”[54] The “dual sovereignty” doctrine is not only tied into the existence of two sets of laws often serving different federal-state purposes and the now overruled principle that the Double Jeopardy Clause restricts only the national government and not the states,[55] but it also reflects practical considerations that undesirable consequences could follow an overruling of the doctrine. Thus, a state might preempt federal authority by first prosecuting and providing for a lenient sentence (as compared to the possible federal sentence) or acquitting defendants who had the sympathy of state authorities as against federal law enforcement.[56] The application of the clause to the states has therefore worked no change in the “dual sovereign” doctrine. 53 260 U.S. 377 (1922). 54 260 U.S. at 382. See also Hebert v. Louisiana, 272 U.S. 312 (1924); Screws v. United States, 325 U.S. 91, 108 (1945); Jerome v. United States, 318 U.S. 101 (1943). 55 Benton v. Maryland, 395 U.S. 784 (1969), extended the clause to the states. 56 Reaffirmation of the doctrine against double jeopardy claims as to the Federal Government and against due process claims as to the states occurred in Abbate v. United States, 359 U.S. 187 (1959), and Bartkus v. Illinois, 359 U.S. 121 (1959), both cases containing extensive discussion and policy analyses. The Justice Department follows a policy of generally not duplicating a state prosecution brought and carried out in good faith, see Petite v. United States, 361 U.S. 529, 531 (1960); Rinaldi v. United States, 434 U.S. 22 (1977), and several provisions of federal law forbid a federal prosecution following a state prosecution. E.g., 18 U.S.C. §§ 659, 660, 1992, 2117. The Brown Commission recommended a general statute to this effect, preserving discretion in federal authorities to proceed upon certification by the Attorney General that a United States interest would be unduly harmed if there were no federal prosecution. NATIONAL COMMISSION ON REFORM OF FEDERAL CRIMINAL LAWS, FINAL REPORT 707 (1971).

The “dual sovereignty” doctrine is not only tied into the existence of two sets of laws often serving different federal-state purposes and the now overruled principle that the Double Jeopardy Clause restricts only the national government and not the states,[55] but it also reflects practical considerations that undesirable consequences could follow an overruling of the doctrine. Thus, a state might preempt federal authority by first prosecuting and providing for a lenient sentence (as compared to the possible federal sentence) or acquitting defendants who had the sympathy of state authorities as against federal law enforcement.[56] 55 Benton v. Maryland, 395 U.S. 784 (1969), extended the clause to the states. 56 Reaffirmation of the doctrine against double jeopardy claims as to the Federal Government and against due process claims as to the states occurred in Abbate v. United States, 359 U.S. 187 (1959), and Bartkus v. Illinois, 359 U.S. 121 (1959), both cases containing extensive discussion and policy analyses. The Justice Department follows a policy of generally not duplicating a state prosecution brought and carried out in good faith, see Petite v. United States, 361 U.S. 529, 531 (1960); Rinaldi v. United States, 434 U.S. 22 (1977), and several provisions of federal law forbid a federal prosecution following a state prosecution. E.g., 18 U.S.C. §§ 659, 660, 1992, 2117. The Brown Commission recommended a general statute to this effect, preserving discretion in federal authorities to proceed upon certification by the Attorney General that a United States interest would be unduly harmed if there were no federal prosecution. NATIONAL COMMISSION ON REFORM OF FEDERAL CRIMINAL LAWS, FINAL REPORT 707 (1971).