Gemara

(Beraisa): If during Shemoneh Esreh one started to urinate, he waits until the urine stops, then resumes praying.

(Rav Chisda or Rav Hamnuna): He returns to the beginning of Shemoneh Esre;

(The other of Rav Chisda and Rav Hamnuna): He returns to the place he stopped.

(Rav Ashi): If he delayed long enough to finish, all agree that he returns to the beginning. They argue about one who delayed less than this:

The first opinion holds that since he was not allowed to pray, his prayer is invalid. The second opinion holds that he was allowed, so his prayer is valid.

24b (Tana): If one feels a need to emit gas during prayer, he walk backs four Amos... wait for the odor to go away, returns and says '... our shame is revealed before You...";

He resumes praying from where he left off.

34a (Rav Huna): If one erred in one of the first three Berachos, he returns to the beginning of Shemoneh Esreh. If one erred in one of the last three, he returns to Retzeh (the first of the last three).

Megilah 18b (Beraisa): One who read the Megilah intermittently was Yotzei;

R. Muna says, if he paused long enough to finish it, he was not Yotzei.

(R. Aba and Rav Kahana citing Rav): The Halachah follows R. Muna;

(Shmuel): The Halachah does not follow R. Muna.

(Rav Bivi): No, Shmuel holds that the Halachah follows R. Muna, and Rav disagrees.

(Rav Yosef): One should follow Rav Bivi, for we know that Shmuel is concerned for an individual's opinion.

Rosh Hashanah 34b (R. Yochanan, and a Beraisa): If one heard the nine required Teki'os at nine times during the day, he was Yotzei.

Contradiction (R. Yochanan citing R. Shimon ben Yehotzadak): If one paused long enough in Hallel or the Megilah to finish all of it, he returns to the beginning.

Answer: R. Yochanan himself holds that he was Yotzei. He said in the name of R. Shimon ben Yehotzadak that he returns to the beginning.

Question: R. Avahu was saying Keri'as Shema. He came to a filthy alley and stopped. He asked R. Yochanan where to resume;

R. Yochanan: If you paused long enough to finish Shema, you resume from the beginning.

Answer: R. Yochanan himself holds that he did not need to stop. He told R. Avahu 'you hold that one must stop. If so, if you paused long enough to finish, you return to the beginning.'

Rishonim

Rif (15b): One who interrupted Keri'as Shema returns to where he stopped, even if he delayed long enough to finish. Rosh Hashanah concludes like this. The same applies to one who interrupted the Teki'os, Hallel or the Megilah. Only for Tefilah, if he delayed long enough to finish, he returns to the beginning.

R. Yonah (16a DH Aval): The Tosafists equate Tefilah, Keri'as Shema and Megilah. One returns to where he stopped.

Rambam (Hilchos Kri'as Shema 2:12): If one read Shma intermittently, he was Yotzei, even if he delayed long enough to finish.

Tosfos (18b DH Nekot): Rav Yosef holds like Rav Bivi, who says that Rav rules that one does not return to the beginning. The Halachah follows Rav in Isurim. Also, R. Yochanan holds like him in Rosh Hashanah. Since a Beraisa supports him, the Halachah follows him. The Ri supports from this waiting in Emes v'Yatziv to say Kedushah, Borchu and Amen Yehei Shmei Raba with the Tzibur.

Rosh (3:23): One opinion forbids praying while urine flows on his leg, therefore he returns to the beginning. He was Dachuy (unable to do the Mitzvah). He is unlike one who came to a filthy alley while saying Shema, who resumes from where he left off if he did not pause long enough to finish. He was Kosher to recite, just the place was not. The other opinion holds that the Torah forbids praying only facing a stream of urine. If it is dripping down his leg, mid'Rabanan he may not begin praying, but if he was praying he could continue.

Rosh (ibid.): For Tefilah, if he delayed long enough to finish, all agree that he returns to the beginning. We could not have said that if he delayed less than this, all agree that he does not return, and they argue about one who delayed. [The one who says that he returns holds that he was Dachuy.] We could not say so, for all agree that he may pray, since some (i.e. a small) interruption does not obligate repeating what he prayed.

Note: Above, the Rosh said that they argue about whether or not he was Dachuy! I.e. the one who says so always requires returning to the beginning. We cannot say that he is Dachuy, but returns to the beginning only for a long delay - PF.

Rosh (ibid.): If we could have said that all agree that if he delayed long enough to finish, he does not return to the beginning, we would have said so, for we hold like this. In Megilah we rule unlike R. Muna. In Rosh Hashanah, R. Yochanan says that one is Yotzei through nine Teki'os heard throughout the day. The Halachah always follows him, especially against R. Avahu, his Talmid. R. Shimshon says that if one chose to pause in the middle long enough to finish, without any Ones, he does not return to the beginning. This is the case in Megilah and Rosh Hashanah. If due to Ones, e.g. he could not pray due to urine on his legs, if he delayed long enough to finish, all agree that he returns to the beginning.

Tosfos (33a DH Aval): The Yerushalmi says that if a snake was heading towards someone praying, he interrupts. It did not say that he returns to the beginning. It seems that he returns to the beginning of the Berachah. If he stopped in one of the first or last three Berachos, he returns to Avos or Retzeh, respectively.

Poskim

Shulchan Aruch (OC 104:5): Whenever one interrupts, if he delayed long enough to finish all of it, he returns to the beginning. If not, he returns to the Berachah in which he stopped.

Beis Yosef (DH uv'Chol, citing the Rashba): The Rif holds that if he delayed long enough to finish all of it, he returns to the beginning. The Ra'avad says so only when the person is Dachuy, e.g. urine was flowing on his legs. Here he returns to where he stopped, even in the middle of a Berachah, like in the middle of Berachos (of Keri'as Shema) one may greet and answer due to fear and honor. Why does Tosfos say that he returns to the beginning of the Berachah?!

Beis Yosef (ibid.): For Tefilah, if he delayed long enough to finish, he returns to the beginning even without Dichuy. If he did not delay so long, we hold like Tosfos and the Rosh), that he returns to the beginning of the Berachah. Surely, Tefilah is more stringent than Keri'as Shema.

Taz (2): The Rif proved that Tefilah is more stringent than Keri'as Shema, for which one returns to where he stopped. The Rema did not need to comment here, for Tosfos and the Rosh agree that he returns to the beginning (for any Ones - Mishbetzos Zahav). The Bach disagreed with the Mechaber and Rema, and said that even if he delayed long enough to finish, he returns to where he stopped. This is wrong. If he delayed long enough to finish, all agree that he returns to the beginning!

Gra (DH Im): He returns to the beginning only if he delayed long enough to finish it all, due to Ones.

Gra (DH Chozer): The Yerushalmi proves that Tefilah is not more stringent. It asked from Tefilah to Keri'as Shema! If one needed to emit gas... he says '... our shame..." and resumes from where he stopped. Rebbi (said the verse of Shma in the middle of teaching, and) later finished Shma (13b), after a great Hefsek If one was proofreading and read Shma, if he intended, he was Yotzei, even though he delayed greatly between Parshiyos (13a). We do not distinguish interrupting for a Mitzvah or Reshus.

Note: One could explain that the Gemara teaches that he was Yotzei the one Parshah he proofread. Perhaps this is why Rashi (13a DH Hayah) explains that he was reading Parshas (singular) Shma.

Gra (65:1 DH v'Yesh): The Ri and Tosfos in Megilah hold that one does not return to the beginning of Tefilah, even if there was Ones. Tosfos in Rosh Hashanah holds that one always returns to the beginning, even without Ones.

Gra (65:1 DH Afilu): The question in Rosh Hashanah from R. Avahu shows that this is even in a case of Ones.

Mishnah Berurah (13): This is even for pausing silently, even between Berachos.

Mishnah Berurah (15): If he delayed long enough to finish all of Tefilah, and returned to where he stopped and finished from there, he must return to the beginning and pray the entire Tefilah. This is if there was total Ones. If it was an Ones like bandits, b'Di'eved he was Yotzei, for perhaps the Halachah follows the lenient opinion that this is not considered Ones.

Kaf ha'Chayim (29): In any case that he returned to where he stopped, since some say that to do so always, and some say that Tefilah is mid'Rabanan, and all agree that the text is mid'Rabanan, we are lenient about Safek Berachos, so he does not pray again.

Mishnah Berurah (16): We hold like the Rema (65:1), that one returns to the beginning in Keri'as Shema only if the delay was due to Ones, and similarly for Tefilah. However, some call a delay due to a scorpion or bandits Ones, for he could not have prayed. Some say that Ones is only if he or the place were not proper for prayer. The Magen Avraham and others hold here like the first opinion, for some Rishonim obligate returning to the beginning if he delayed long enough to finish, even without any Ones. For Keri'as Shema, it is Ones only if he or the place was not proper.

Kaf ha'Chayim (28): Also the Prishah and Eliyahu Rabah hold like the Taz, that even Ones due to a scorpion is called Ones. It seems that the Rosh and Avudraham agree. In Siman 90, the Mechaber (in Bedek ha'Bayis) rules like R. Yonah, that even if he delayed long enough to finish, even due to Ones, he returns to where he stopped. Why does he rule differently here? Some say that here he interrupted through speech. It seems that we distinguish like this.

Mishnah Berurah (17): If he delayed long enough to finish a Berachah, but not all of Tefilah, all agree that he returns to where he stopped.

Mishnah Berurah (18): Here, a delay in a Berachah ruins the Berachah, so he returns to the beginning of the Berachah. Keri'as Shema is different.

Mishnah Berurah (19): The Chayei Adam says that if he did not return to the beginning of the Berachah, rather, to where he stopped, and finished it, he may not repeat it. Magen Giborim says that he returns to where he stopped. Tosfos says that he returns to the beginning if he delayed long enough to finish everything. The Gra holds that he always returns to where he stopped, unless he delayed long enough to finish everything, due to Ones.

Shulchan Aruch (ibid.): If he stopped in one of the first three Berachos, he returns to the beginning. If he stopped in one of the last (three) Berachos, he returns to Retzeh.

Beis Yosef (DH Kasav): The Avudraham brings from R. Gershom that if one talked in the middle, he returns to the beginning, for all 18 Berachos are like one. Orchos Chayim says so in the name of the Ra'avad. The Poskim disagree. One could distinguish, for they discussed Reshus, but it seems that one does not return to the beginning. All 18 Berachos are not like one. Only the first three and last three are like one!

Mishnah Berurah (20): According to the Gra, he returns to where he stopped.

Mishnah Berurah (21): The Chayei Adam says that he returns to the beginning only if he finished the Berachah. If he was in the middle, he returns the beginning of that Berachah, for this is not called returning. It is fixing his words.