Gemara

22b (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: R. Avahu was walking behind R. Yochanan and saying Keri'as Shema. He came to a filthy alley and stopped. Later, he asked where to resume;

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

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 resume from the beginning.'

Rishonim

Rif and Rosh (14a and 3:23, b'Sof): Rav Hai Gaon rules like the opinion that he returns to where he stopped. If he delayed long enough to finish, he returns to the beginning.

Rif (15b): One who interrupted Keri'as Shema returns to where he stopped, even if he delayed long enough to finish. Only regarding 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. He 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.

Hagahos Maimoniyos (30/60): Avi ha'Ezri does not distinguish whether he interrupted in silence, or he spoke. (Rashi said oppositely (i.e. it is a problem only if he spoke. The Tur says that one should be concerned for both opinions. - this is not in all editions of Hagahos Maimoniyos.)

Tosfos (24b DH Amar): R. Yochanan disagreed with R. Avahu about two matters. R. Yochanan holds that one returns to where he stopped, and that one may read in a filthy place.

Rebuttal (Rosh 3:23, citing R. Shimshon of Kutzi): If a Talmid was unsure and asked, it is not normal to answer him based on his reasoning! Also, what is the source that R. Avahu holds that one who delayed long enough to finish returns to the beginning? R. Shimshon answered that if one delayed in the middle long enough to finish, without any Dichuy (inability to do the Mitzvah) or Ones, rather, he decided to pause, he does not return to the beginning. If he delayed due to Ones, e.g. urine was on his legs and he could not pray at the time, all agree that if he delayed long enough to finish, he returns to the beginning. This is why R. Yochanan told R. Avahu 'according to you, you must return to the beginning.'

Me'iri (Magen Avos, Sof Inyan 1): R. Avahu's question was not a Hefsek, because it was needed for the matter (to know to where to return).

Mordechai and Tosfos (Rosh Hashanah 721 and 32b DH l'Didi): It is very difficult that the Tzibur waits while the Shali'ach Tzibur finishes (the Piyut) Zulas. If they do not wait long enough to finish all of it from the beginning to the end, we are not concerned. We do not gauge from where he is to the end.

Magen Avraham (OC 65:1): This connotes l'Chatchilah, one may not delay even not due to Ones, even in Birkos Keri'as Shema. See what I wrote in 53:1. (One stands during Yishtabach, to avoid the need to pause before it and Kaddish.) However, (if he delays) in order to answer to Kaddish or Kedushah, he may delay even long enough to finish all of it.

Poskim

Shulchan Aruch (OC 65:1): If one read Shma intermittently, i.e. he began to read and interrupted, whether silently or spoke, and he later finished, even if he delayed long enough to finish all of it, he was Yotzei, even if he paused due to Ones.

Beis Yosef (DH Kar'ah): The Rif and Rambam rule that one always returns to where he stopped, except for Tefilah. Tosfos, the Rashba in the name of the Ra'avad, the Rosh and Tur rule like R. Shimshon, that if he delayed long enough to finish the entire matter due to Ones, he returns to the beginning. R. Yonah cites the Tosafists to say that even for Tefilah he returns to where he stopped. He did not distinguish whether or not he paused due to Ones. The Rif and Rambam hold like this. This is the Halachah.

Gra (DH Bein): We find that (sometimes, in Birkos Keri'as Shema) one may greet and answer. If one would need to return to the beginning, it would be forbidden, just like regarding Tefilin (Menachos 36a. One may not talk in between the hand head and head Tefilin, for then he must bless again.)

Mishnah Berurah (1): Even if one talked b'Mezid, even though he transgressed, he returns to where he stopped, even in the middle of a Berachah. The same applies to one who talked in the middle of Hallel, Megilah, Birkas ha'Mazon or any long Berachah. This is only if he says it himself. If he is Yotzei through hearing from someone else, and he talked in the middle, he did not hear, so he cannot be Yotzei.

Mishnah Berurah (2): The Magen Avraham holds that pausing is a Hefsek only if it was due to Ones, that it was Asur for him to read at the time. This is only for Keri'as Shema and its Berachos. For Tefilah, he returns to the beginning for any Ones.

Rema: Some say that if due to Ones he delayed long enough to finish all of it, he returns to the beginning. This is the custom.

Magen Avraham (2): The Tur, Tosfos and Rosh connote that even if the Ones is due to bandits or an extortionist, he returns to the beginning. Maharam Mintz (85) says that if two people quarreled and interrupted, this is not Dichuy, for they could have made peace at any time (and resumed reading). This implies that if the Ones was due to someone else, he returns to the beginning. The Bach says that Ones is only if the person or place was not proper to read. One does not return to the beginning for other Onesim. The Beis Yosef (114) brings from the Ra'avad that Ones is only when the person is Dachuy, e.g. urine was flowing on his legs. From the beginning he could not pray, since he needed to relieve himself. If not, he does not return to the beginning. Also Ba'al ha'Ma'or says so. The Rashba says that a person is Dachuy when urine flows on his legs. He could not pray at the time. This is like Tosfos. I say that if one delayed long enough to finish all of Tefilah, even due to other Ones, he returns to the beginning, since the Rif and those who agree with him say so even without Ones. Also, it would be great if a person prayed the entire day (21a)! For Keri'as Shema, he returns only if the person or place was not proper to say Shma.

Mishnah Berurah (4): L'Chatchilah, one may not delay long enough to finish all of it, even not due to Ones, even in silence. This is even for something mid'Rabanan, such as Birkos Keri'as Shema, Hallel and Megilah. All the more so one must be careful about Tefilah, for some are stringent about Tefilah even b'Di'eved. The Magen Avraham connotes that l'Chatchilah, the Shali'ach Tzibur should not sing at length in Birkos Keri'as Shema (so that people pause) at once long enough to finish all of it. [All the more so the Tzibur should be careful in Birkas Kohanim, which is mid'Oraisa, not to prolong the supplications, for then the Kohanim must wait in the middle of the Berachah. Therefore, one should do like the Gra says [also the Rema 128:45 connotes like him]. Even in the third Berachah, the Tzibur should say 'Ribono Shel Olam...', and not the long 'Yehi Ratzon...', for often the Kohanim do not sing (the Nigun) and wait silently long enough to finish the Berachah. In order to answer to Kaddish or Kedushah, one may delay even long enough to finish all of it. Shulchan Shlomo says that this is only if he is at the end of Emes v'Yatziv, i.e. Shirah Chdashah. If not, it is better to break up the pauses in the middle of the Berachah, so no pause is enough to finish all of it.

Mishnah Berurah (5): If he paused in Keri'as Shema long enough to finish Keri'as Shema, he returns to the beginning. If he paused in a Berachah of Keri'as Shema, he returns to the beginning of the Berachah only if he paused long enough to finish from Yotzer Ohr to Ga'al Yisrael. B'Di'eved, one never need return due a pause between Berachos of Keri'as Shema. If one paused between Parshiyos of Shma due to Ones, long enough to finish all the Parshiyos, he returns to the beginning.

Kaf ha'Chayim (3): The Levush, Bach and Magen Avraham rule like the Rema, and this is the custom of Ashkenazim. The Pri Chodosh, Aruch ha'Shulchan and Sidur Beis Yakov rule like the Mechaber. This is primary.

Bi'ur Halachah (DH Bein): The Magen Avraham (104:6) concluded that if one talked in Keri'as Shema or its Berachos, but he did not delay long enough to finish, he does not return to the beginning. We consider him like Shogeg, because most people are not careful about this. This implies that where people are careful, or if he knew the law, he is totally Mezid and he returns to the beginning, like for Tefilah. He rules like this (183:11) for Birkas ha'Mazon. The Gra holds that he returns to where he stopped (regarding Tefilah). The same applies to Birkas ha'Mazon. Even though it is mid'Oraisa, it is not more stringent than Keri'as Shema. Also Eliyahu Rabah questioned the Magen Avraham. It is hard to rule like the Magen Avraham in practice. Many say that even for Tefilah, he was Yotzei even if he talked b'Mezid. I say that b'Di'eved he does not return. For the Parshiyos of Keri'as Shema, he should be stringent to repeat them. He should not repeat Berachos.

Rema (ibid.): We estimate the delay based on the one who read, and not based on most people. The same applies in Siman 104:5,6.

Gra (DH u'Mesha'arin): The Yerushalmi says that we estimate based on the one who reads.