The news article here refers back to a Deferred Prosecution Agreement from 2021, between the US Department of Justice and Boeing. The fresh statement from the DoJ is to the effect that if Boeing has breached the terms of that agreement, then the DoJ might take up the prosecution again. See a DoJ press release from 2021 for the context of the original agreement.
Such agreements are essentially "so long as you do X, we will not prosecute you for Y". They have legal effect in that once the promise has been made, and if Boeing has indeed done X, then the courts would not allow a prosecution for Y to go forward. Some typical conditions for X are:
- make public statements admitting the relevant facts behind Y
- paying some money in fines
- paying some money to compensate victims
- taking steps to avoid future similar crimes (e.g. corporate restructuring)
- making regular reports on progress implementing the changes
- paying costs of the criminal investigation and prosecution
- cooperating with ongoing related investigations
- cooperating with an independent monitor
The Department of Justice is now saying that Boeing might not have done X to its satisfaction, and so the company can potentially be prosecuted for Y. In procedural terms, this is not bringing a fresh charge, but would be reviving a criminal case that was previously filed and put on hold: so it's about going back to the original court and arguing what should happen. Again because of that implementing procedure, the DPA does not deal with a completely separate crime involving Boeing - that would be a new indictment for something else - or with proceedings before a foreign court. It's strictly about the DoJ setting limits on its own specific ongoing prosecution.
For the question at hand, the charge of Y in this case was that Boeing defrauded an agency of the US Government (the Federal Aviation Administration) concerning the safety of the 737 MAX aircraft. The conduct in question took place well before either of the two aircraft crashes. Partly because of those crashes, taking place in Indonesia and Ethiopia, the FAA came to learn that Boeing had misled it. The criminal fraud charge here is not "Boeing crashed some planes (outside the USA)" but "Boeing lied to the FAA". Those lies probably took place in the USA, but even if they didn't, the federal courts have subject-matter jurisdiction over the offense in question, "conspiracy to defraud the United States" (18 USC 371). It's one of those crimes which can be prosecuted federally even if committed somewhere else in the world.
If a trial were to go forward, then there is no problem with the federal courts receiving evidence of the events taking place in Indonesia or Ethopia. Indeed, there are specific rules about, for example, documentary evidence produced by a foreign government - such as a report into a plane crash.
The scope of the DPA does not protect Boeing from prosecution for other crimes, or from civil liability related to its conduct. In other instances, US courts have had jurisdiction for different reasons. For example, some wrongful death claims from the Lion Air crash were heard by federal courts because of the Death on the High Seas Act, which is a US statute concerning this sort of situation. Boeing is also being sued by some of its shareholders for securities fraud relating to the crashes: in that case, the alleged bad conduct is that Boeing made knowingly false public assurances about safety, causing the stock price to be inflated (and it then dropped once the rest of the world caught up to Boeing's state of knowledge).